data_SRY
#
_chem_comp.id SRY
_chem_comp.name STREPTOMYCIN
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C21 H39 N7 O12"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "STREPTOMYCIN A"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-08-25
_chem_comp.pdbx_modified_date 2020-06-17
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 581.574
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SRY
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1NTA
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
SRY C11 C11 C 0 1 N N R N N N 6.651 34.161 -1.203 -4.507 0.184 -0.242 C11 SRY 1
SRY N11 N11 N 0 1 N N N N N N 7.760 33.416 -0.486 -5.686 0.670 -0.963 N11 SRY 2
SRY CA1 CA1 C 0 1 N N N N N N 8.902 33.432 -1.157 -6.824 -0.099 -1.017 CA1 SRY 3
SRY NB1 NB1 N 0 1 N N N N N N 9.591 34.506 -1.048 -6.856 -1.324 -0.394 NB1 SRY 4
SRY NC1 NC1 N 0 1 N N N N N N 9.292 32.429 -1.867 -7.873 0.334 -1.659 NC1 SRY 5
SRY C21 C21 C 0 1 N N R N N N 5.865 35.030 -0.203 -3.657 1.374 0.207 C21 SRY 6
SRY O21 O21 O 0 1 N N N N N N 6.753 35.981 0.302 -4.429 2.213 1.068 O21 SRY 7
SRY C31 C31 C 0 1 N N S N N N 4.712 35.791 -0.871 -2.425 0.866 0.961 C31 SRY 8
SRY N31 N31 N 0 1 N N N N N N 3.930 36.635 0.064 -1.611 2.006 1.390 N31 SRY 9
SRY CD1 CD1 C 0 1 N N N N N N 3.954 36.163 1.265 -1.902 2.653 2.568 CD1 SRY 10
SRY NE1 NE1 N 0 1 N N N N N N 4.748 35.211 1.681 -1.138 3.722 2.971 NE1 SRY 11
SRY NF1 NF1 N 0 1 N N N N N N 3.107 36.677 2.068 -2.902 2.252 3.302 NF1 SRY 12
SRY C41 C41 C 0 1 N N R N N N 3.786 34.772 -1.516 -1.599 -0.033 0.039 C41 SRY 13
SRY O41 O41 O 0 1 N N N N N N 2.724 35.481 -2.135 -0.449 -0.507 0.743 O41 SRY 14
SRY C51 C51 C 0 1 N N R N N N 4.566 33.922 -2.559 -2.449 -1.223 -0.410 C51 SRY 15
SRY O51 O51 O 0 1 N N N N N N 3.679 32.980 -3.160 -1.676 -2.063 -1.270 O51 SRY 16
SRY C61 C61 C 0 1 N N S N N N 5.708 33.167 -1.847 -3.680 -0.715 -1.163 C61 SRY 17
SRY O61 O61 O 0 1 N N N N N N 6.441 32.374 -2.795 -4.474 -1.827 -1.582 O61 SRY 18
SRY C12 C12 C 0 1 N N R N N N 1.451 35.087 -1.593 0.684 -0.752 -0.093 C12 SRY 19
SRY C22 C22 C 0 1 N N S N N N 0.436 36.009 -2.260 1.910 -1.140 0.763 C22 SRY 20
SRY C32 C32 C 0 1 N N S N N N -0.011 35.173 -3.379 1.893 -2.684 0.766 C32 SRY 21
SRY O32 O32 O 0 1 N N N N N N -1.371 34.816 -3.124 3.085 -3.200 0.168 O32 SRY 22
SRY CG2 CG2 C 0 1 N N N N N N 0.141 35.947 -4.661 1.739 -3.208 2.170 CG2 SRY 23
SRY OG2 OG2 O 0 1 N N N N N N -0.096 35.511 -5.766 0.791 -3.898 2.457 OG2 SRY 24
SRY C42 C42 C 0 1 N N S N N N 0.795 33.946 -3.401 0.659 -3.048 -0.089 C42 SRY 25
SRY CH2 CH2 C 0 1 N N N N N N 0.177 32.698 -3.951 0.943 -4.291 -0.935 CH2 SRY 26
SRY O42 O42 O 0 1 N N N N N N 1.203 33.777 -2.049 0.447 -1.899 -0.938 O42 SRY 27
SRY O13 O13 O 0 1 N N N N N N -0.430 36.466 -1.371 3.113 -0.653 0.163 O13 SRY 28
SRY C13 C13 C 0 1 N N S N N N 0.183 37.124 -0.318 3.562 0.596 0.692 C13 SRY 29
SRY C23 C23 C 0 1 N N S N N N 0.101 38.634 -0.362 5.014 0.837 0.271 C23 SRY 30
SRY N23 N23 N 0 1 N N N N N N 0.622 39.082 -1.607 5.851 -0.276 0.739 N23 SRY 31
SRY CI3 CI3 C 0 1 N N N N N N 2.032 39.369 -1.403 6.284 -0.061 2.126 CI3 SRY 32
SRY C33 C33 C 0 1 N N S N N N -1.212 39.067 -0.241 5.087 0.925 -1.257 C33 SRY 33
SRY O33 O33 O 0 1 N N N N N N -1.183 40.450 0.007 6.426 1.222 -1.655 O33 SRY 34
SRY C43 C43 C 0 1 N N R N N N -1.892 38.365 0.905 4.150 2.037 -1.738 C43 SRY 35
SRY O43 O43 O 0 1 N N N N N N -3.262 38.635 0.854 4.155 2.081 -3.166 O43 SRY 36
SRY C53 C53 C 0 1 N N S N N N -1.700 36.892 0.779 2.731 1.750 -1.240 C53 SRY 37
SRY O53 O53 O 0 1 N N N N N N -0.327 36.633 0.835 2.740 1.650 0.186 O53 SRY 38
SRY C63 C63 C 0 1 N N N N N N -2.366 36.138 1.947 1.801 2.888 -1.665 C63 SRY 39
SRY O63 O63 O 0 1 N N N N N N -2.278 36.930 3.126 0.457 2.566 -1.302 O63 SRY 40
SRY H11 H11 H 0 1 N N N N N N 7.096 34.807 -1.974 -4.825 -0.386 0.632 H11 SRY 41
SRY HN11 1HN1 H 0 0 N N N N N N 7.642 32.962 0.397 -5.663 1.534 -1.403 HN11 SRY 42
SRY HB11 1HB1 H 0 0 N N N N N N 10.434 34.440 -1.581 -6.076 -1.646 0.084 HB11 SRY 43
SRY HB12 2HB1 H 0 0 N N N N N N 9.323 35.301 -0.504 -7.660 -1.866 -0.432 HB12 SRY 44
SRY HC11 1HC1 H 0 0 N N N N N N 8.623 31.687 -1.826 -7.850 1.198 -2.098 HC11 SRY 45
SRY H21 H21 H 0 1 N N N N N N 5.442 34.373 0.571 -3.339 1.943 -0.666 H21 SRY 46
SRY HO21 1HO2 H 0 0 N N N N N N 6.955 35.777 1.208 -5.227 2.572 0.655 HO21 SRY 47
SRY H31 H31 H 0 1 N N N N N N 5.155 36.477 -1.608 -2.743 0.297 1.834 H31 SRY 48
SRY HN31 1HN3 H 0 0 N N N N N N 3.444 37.467 -0.203 -0.867 2.304 0.844 HN31 SRY 49
SRY HE11 1HE1 H 0 0 N N N N N N 4.611 34.989 2.646 -0.394 4.020 2.425 HE11 SRY 50
SRY HE12 2HE1 H 0 0 N N N N N N 5.420 34.755 1.097 -1.343 4.179 3.802 HE12 SRY 51
SRY HF11 1HF1 H 0 0 N N N N N N 2.549 37.386 1.637 -3.441 1.498 3.018 HF11 SRY 52
SRY H41 H41 H 0 1 N N N N N N 3.385 34.081 -0.760 -1.281 0.536 -0.835 H41 SRY 53
SRY H51 H51 H 0 1 N N N N N N 4.984 34.580 -3.335 -2.767 -1.792 0.464 H51 SRY 54
SRY HO51 1HO5 H 0 0 N N N N N N 3.482 33.252 -4.049 -2.153 -2.839 -1.594 HO51 SRY 55
SRY H61 H61 H 0 1 N N N N N N 5.274 32.511 -1.078 -3.362 -0.146 -2.037 H61 SRY 56
SRY HO61 1HO6 H 0 0 N N N N N N 6.603 32.886 -3.579 -4.012 -2.440 -2.170 HO61 SRY 57
SRY H12 H12 H 0 1 N N N N N N 1.409 35.136 -0.495 0.906 0.127 -0.698 H12 SRY 58
SRY H22 H22 H 0 1 N N N N N N 0.778 36.974 -2.663 1.805 -0.754 1.777 H22 SRY 59
SRY HO32 2HO3 H 0 0 N N N N N N -1.508 34.737 -2.187 3.127 -4.165 0.144 HO32 SRY 60
SRY HG21 1HG2 H 0 0 N N N N N N 0.487 36.968 -4.590 2.477 -2.966 2.921 HG21 SRY 61
SRY H42 H42 H 0 1 N N N N N N 1.611 34.087 -4.125 -0.209 -3.215 0.549 H42 SRY 62
SRY HH21 1HH2 H 0 0 N N N N N N 0.025 32.810 -5.035 1.181 -5.129 -0.280 HH21 SRY 63
SRY HH22 2HH2 H 0 0 N N N N N N 0.844 31.844 -3.761 0.064 -4.534 -1.531 HH22 SRY 64
SRY HH23 3HH2 H 0 0 N N N N N N -0.792 32.523 -3.462 1.788 -4.095 -1.596 HH23 SRY 65
SRY H13 H13 H 0 1 N N N N N N 1.262 36.926 -0.395 3.497 0.575 1.780 H13 SRY 66
SRY H23 H23 H 0 1 N N N N N N 0.682 39.044 0.477 5.370 1.770 0.708 H23 SRY 67
SRY HN23 3HN2 H 0 0 N N N N N N 0.510 38.374 -2.304 5.369 -1.157 0.643 HN23 SRY 68
SRY HI31 1HI3 H 0 0 N N N N N N 2.537 39.442 -2.378 6.862 0.861 2.188 HI31 SRY 69
SRY HI32 2HI3 H 0 0 N N N N N N 2.138 40.322 -0.864 5.410 0.014 2.772 HI32 SRY 70
SRY HI33 3HI3 H 0 0 N N N N N N 2.489 38.561 -0.813 6.903 -0.900 2.447 HI33 SRY 71
SRY H33 H33 H 0 1 N N N N N N -1.770 38.844 -1.162 4.779 -0.026 -1.692 H33 SRY 72
SRY HO33 3HO3 H 0 0 N N N N N N -1.176 40.604 0.944 6.546 1.293 -2.612 HO33 SRY 73
SRY H43 H43 H 0 1 N N N N N N -1.462 38.719 1.854 4.489 2.995 -1.343 H43 SRY 74
SRY HO43 3HO4 H 0 0 N N N N N N -3.606 38.696 1.737 3.582 2.764 -3.541 HO43 SRY 75
SRY H53 H53 H 0 1 N N N N N N -2.151 36.556 -0.166 2.378 0.812 -1.668 H53 SRY 76
SRY H631 1H63 H 0 0 N N N N N N -3.423 35.949 1.708 2.101 3.809 -1.166 H631 SRY 77
SRY H632 2H63 H 0 0 N N N N N N -1.853 35.178 2.108 1.863 3.023 -2.745 H632 SRY 78
SRY HO63 3HO6 H 0 0 N N N N N N -2.258 36.363 3.888 -0.189 3.244 -1.543 HO63 SRY 79
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
SRY C11 N11 SING N N 1
SRY C11 C21 SING N N 2
SRY C11 C61 SING N N 3
SRY C11 H11 SING N N 4
SRY N11 CA1 SING N N 5
SRY N11 HN11 SING N N 6
SRY CA1 NB1 SING N N 7
SRY CA1 NC1 DOUB N N 8
SRY NB1 HB11 SING N N 9
SRY NB1 HB12 SING N N 10
SRY NC1 HC11 SING N N 11
SRY C21 O21 SING N N 12
SRY C21 C31 SING N N 13
SRY C21 H21 SING N N 14
SRY O21 HO21 SING N N 15
SRY C31 N31 SING N N 16
SRY C31 C41 SING N N 17
SRY C31 H31 SING N N 18
SRY N31 CD1 SING N N 19
SRY N31 HN31 SING N N 20
SRY CD1 NE1 SING N N 21
SRY CD1 NF1 DOUB N N 22
SRY NE1 HE11 SING N N 23
SRY NE1 HE12 SING N N 24
SRY NF1 HF11 SING N N 25
SRY C41 O41 SING N N 26
SRY C41 C51 SING N N 27
SRY C41 H41 SING N N 28
SRY O41 C12 SING N N 29
SRY C51 O51 SING N N 30
SRY C51 C61 SING N N 31
SRY C51 H51 SING N N 32
SRY O51 HO51 SING N N 33
SRY C61 O61 SING N N 34
SRY C61 H61 SING N N 35
SRY O61 HO61 SING N N 36
SRY C12 C22 SING N N 37
SRY C12 O42 SING N N 38
SRY C12 H12 SING N N 39
SRY C22 C32 SING N N 40
SRY C22 O13 SING N N 41
SRY C22 H22 SING N N 42
SRY C32 O32 SING N N 43
SRY C32 CG2 SING N N 44
SRY C32 C42 SING N N 45
SRY O32 HO32 SING N N 46
SRY CG2 OG2 DOUB N N 47
SRY CG2 HG21 SING N N 48
SRY C42 CH2 SING N N 49
SRY C42 O42 SING N N 50
SRY C42 H42 SING N N 51
SRY CH2 HH21 SING N N 52
SRY CH2 HH22 SING N N 53
SRY CH2 HH23 SING N N 54
SRY O13 C13 SING N N 55
SRY C13 C23 SING N N 56
SRY C13 O53 SING N N 57
SRY C13 H13 SING N N 58
SRY C23 N23 SING N N 59
SRY C23 C33 SING N N 60
SRY C23 H23 SING N N 61
SRY N23 CI3 SING N N 62
SRY N23 HN23 SING N N 63
SRY CI3 HI31 SING N N 64
SRY CI3 HI32 SING N N 65
SRY CI3 HI33 SING N N 66
SRY C33 O33 SING N N 67
SRY C33 C43 SING N N 68
SRY C33 H33 SING N N 69
SRY O33 HO33 SING N N 70
SRY C43 O43 SING N N 71
SRY C43 C53 SING N N 72
SRY C43 H43 SING N N 73
SRY O43 HO43 SING N N 74
SRY C53 O53 SING N N 75
SRY C53 C63 SING N N 76
SRY C53 H53 SING N N 77
SRY C63 O63 SING N N 78
SRY C63 H631 SING N N 79
SRY C63 H632 SING N N 80
SRY O63 HO63 SING N N 81
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
SRY SMILES ACDLabs 10.04 O=CC3(O)C(OC1OC(C(O)C(O)C1NC)CO)C(OC2C(NC(=[N@H])N)C(O)C(NC(=[N@H])N)C(O)C2O)OC3C
SRY InChI InChI 1.03 InChI=1S/C21H39N7O12/c1-5-21(36,4-30)16(40-17-9(26-2)13(34)10(31)6(3-29)38-17)18(37-5)39-15-8(28-20(24)25)11(32)7(27-19(22)23)12(33)14(15)35/h4-18,26,29,31-36H,3H2,1-2H3,(H4,22,23,27)(H4,24,25,28)/t5-,6-,7+,8-,9-,10-,11+,12-,13-,14+,15+,16-,17-,18-,21+/m0/s1
SRY InChIKey InChI 1.03 UCSJYZPVAKXKNQ-HZYVHMACSA-N
SRY SMILES_CANONICAL CACTVS 3.385 CN[C@H]1[C@H](O)[C@@H](O)[C@H](CO)O[C@H]1O[C@H]2[C@@H](O[C@@H](C)[C@]2(O)C=O)O[C@H]3[C@H](O)[C@@H](O)[C@H](NC(N)=N)[C@@H](O)[C@@H]3NC(N)=N
SRY SMILES CACTVS 3.385 CN[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[CH]2[CH](O[CH](C)[C]2(O)C=O)O[CH]3[CH](O)[CH](O)[CH](NC(N)=N)[CH](O)[CH]3NC(N)=N
SRY SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "[H]/N=C(/N)\N[C@@H]1[C@H]([C@@H]([C@H]([C@@H]([C@H]1O)O)O[C@H]2[C@@H]([C@]([C@@H](O2)C)(C=O)O)O[C@H]3[C@H]([C@@H]([C@H]([C@@H](O3)CO)O)O)NC)N/C(=N\[H])/N)O"
SRY SMILES "OpenEye OEToolkits" 1.7.5 CC1C(C(C(O1)OC2C(C(C(C(C2O)O)NC(=N)N)O)NC(=N)N)OC3C(C(C(C(O3)CO)O)O)NC)(C=O)O
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
SRY "SYSTEMATIC NAME" ACDLabs 10.04 "N,N'''-[(1R,2R,3S,4R,5R,6S)-4-({5-deoxy-2-O-[2-deoxy-2-(methylamino)-alpha-L-glucopyranosyl]-3-C-formyl-alpha-L-lyxofuranosyl}oxy)-2,5,6-trihydroxycyclohexane-1,3-diyl]diguanidine"
SRY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1-[(1R,2R,3S,4R,5R,6S)-3-carbamimidamido-4-[(2R,3R,4R,5S)-3-[(2S,3S,4S,5R,6S)-4,5-dihydroxy-6-(hydroxymethyl)-3-methylamino-oxan-2-yl]oxy-4-hydroxy-4-methanoyl-5-methyl-oxolan-2-yl]oxy-2,5,6-trihydroxy-cyclohexyl]guanidine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SRY 'Create component' 2000-08-25 EBI
SRY 'Modify descriptor' 2011-06-04 RCSB
SRY 'Modify descriptor' 2012-01-05 RCSB
SRY 'Modify coordinates' 2012-01-05 RCSB
SRY 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SRY
_pdbx_chem_comp_synonyms.name "STREPTOMYCIN A"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id SRY
_pdbe_chem_comp_drugbank_details.drugbank_id DB01082
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Streptomycin
_pdbe_chem_comp_drugbank_details.description
'Streptomycin, an antibiotic derived from _Streptomyces griseus_, was the first aminoglycoside to be discovered and used in practice in the 1940s.[A233325,A233390] Selman Waksman and eventually Albert Schatz were recognized with the Nobel Prize in Medicine for their discovery of streptomycin and its antibacterial activity.[A233325,A232294] Although streptomycin was the first antibiotic determined to be effective against mycobacterium tuberculosis, it has fallen out of favor due to resistance and is now primarily used as adjunctive treatment in cases of multi-drug resistant tuberculosis.[A233325]'
_pdbe_chem_comp_drugbank_details.cas_number 57-92-1
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'There are 3 key phases of aminoglycoside entry into cells.[A232294] The first “ionic binding phase” occurs when polycationic aminoglycosides bind electrostatically to negatively charged components of bacterial cell membranes including with lipopolysaccharides and phospholipids within the outer membrane of Gram-negative bacteria and to teichoic acids and phospholipids within the cell membrane of Gram-positive bacteria. This binding results in displacement of divalent cations and increased membrane permeability, allowing for aminoglycoside entry.[A232294, A232304, A232309, A232314]  The second “energy-dependent phase I” of aminoglycoside entry into the cytoplasm relies on the proton-motive force and allows a limited amount of aminoglycoside access to its primary intracellular target - the bacterial 30S ribosome.[A232294, A232314] This ultimately results in the mistranslation of proteins and disruption of the cytoplasmic membrane.[A233320] Finally, in the “energy-dependent phase II” stage, concentration-dependent bacterial killing is observed. Aminoglycoside rapidly accumulates in the cell due to the damaged cytoplasmic membrane, and protein mistranslation and synthesis inhibition is amplified.[A232294, A232314, A232319]  Hence, aminoglycosides have both immediate bactericidal effects through membrane disruption and delayed bactericidal effects through impaired protein synthesis; observed experimental data and mathematical modeling support this two-mechanism model.[A232294, A232299]  Inhibition of protein synthesis is a key component of aminoglycoside efficacy. Structural and cell biological studies suggest that aminoglycosides bind to the 16S rRNA in helix 44 (h44), near the A site of the 30S ribosomal subunit, altering interactions between h44 and h45. This binding also displaces two important residues, A1492 and A1493, from h44, mimicking normal conformational changes that occur with successful codon-anticodon pairing in the A site.[A232324, A232329] Overall, aminoglycoside binding has several negative effects including inhibition of translation, initiation, elongation, and ribosome recycling.[A232294, A232334, A232339] Recent evidence suggests that the latter effect is due to a cryptic second binding site situated in h69 of the 23S rRNA of the 50S ribosomal subunit.[A232329, A232339] Also, by stabilizing a conformation that mimics correct codon-anticodon pairing, aminoglycosides promote error-prone translation.[A232344] Mistranslated proteins can incorporate into the cell membrane, inducing the damage discussed above.[A232294, A232319]'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
SRY 'STREPTOMYCIN A' wwPDB ?
SRY '2,4-diguanidino-3,5,6-trihydroxycyclohexyl 5-deoxy-2-O-(2-deoxy-2-methylamino-alpha-L-glucopyranosyl)-3-C-formyl-beta-L-lyxopentanofuranoside' DrugBank ?
SRY Streptomycin DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id SRY
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01082
_pdbe_chem_comp_drugbank_classification.parent 'Aminocyclitol glycosides'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organooxygen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
SRY DB01082 'Small ribosomal subunit protein uS12' 'Escherichia coli (strain K12)' P0A7S3 yes 1
SRY DB01082 'Protein-arginine deiminase type-4' Humans Q9UM07 no 2
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
SRY C11 C 14.986 3.195 1
SRY N11 N 16.101 4.199 2
SRY CA1 C 17.568 4.511 3
SRY NB1 N 18.031 5.938 4
SRY NC1 N 18.572 3.396 5
SRY C21 C 13.559 3.659 6
SRY O21 O 13.768 5.144 7
SRY C31 C 12.444 2.655 8
SRY N31 N 11.018 3.119 9
SRY CD1 C 10.706 4.586 10
SRY NE1 N 9.280 5.049 11
SRY NF1 N 11.410 5.910 12
SRY C41 C 12.757 1.188 13
SRY O41 O 11.642 0.184 14
SRY C51 C 14.183 0.724 15
SRY O51 O 14.495 -0.743 16
SRY C61 C 15.298 1.728 17
SRY O61 O 16.724 1.264 18
SRY C12 C 10.215 0.648 19
SRY C22 C 9.002 -0.234 20
SRY C32 C 7.788 0.648 21
SRY O32 O 6.906 -0.566 22
SRY CG2 C 6.362 1.111 23
SRY OG2 O 5.247 0.108 24
SRY C42 C 8.252 2.074 25
SRY CH2 C 7.370 3.288 26
SRY O42 O 9.752 2.074 27
SRY O13 O 9.002 -1.734 28
SRY C13 C 7.702 -2.484 29
SRY C23 C 7.702 -3.984 30
SRY N23 N 9.002 -4.734 31
SRY CI3 C 9.002 -6.234 32
SRY C33 C 6.404 -4.734 33
SRY O33 O 6.404 -6.234 34
SRY C43 C 5.104 -3.984 35
SRY O43 O 3.805 -4.734 36
SRY C53 C 5.104 -2.484 37
SRY O53 O 6.404 -1.734 38
SRY C63 C 3.805 -1.734 39
SRY O63 O 3.805 -0.234 40
SRY HC11 H 18.108 1.970 41
SRY HF11 H 12.909 5.963 42
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
SRY C11 N11 SINGLE BEGINWEDGE 1
SRY C11 C21 SINGLE NONE 2
SRY C11 C61 SINGLE NONE 3
SRY N11 CA1 SINGLE ENDUPRIGHT 4
SRY CA1 NB1 SINGLE ENDUPRIGHT 5
SRY CA1 NC1 DOUBLE NONE 6
SRY C21 O21 SINGLE BEGINDASH 7
SRY C21 C31 SINGLE NONE 8
SRY C31 N31 SINGLE BEGINWEDGE 9
SRY C31 C41 SINGLE NONE 10
SRY N31 CD1 SINGLE ENDUPRIGHT 11
SRY CD1 NE1 SINGLE ENDUPRIGHT 12
SRY CD1 NF1 DOUBLE NONE 13
SRY C41 O41 SINGLE BEGINDASH 14
SRY C41 C51 SINGLE NONE 15
SRY C12 O41 SINGLE BEGINWEDGE 16
SRY C51 O51 SINGLE BEGINWEDGE 17
SRY C51 C61 SINGLE NONE 18
SRY C61 O61 SINGLE BEGINDASH 19
SRY C12 C22 SINGLE NONE 20
SRY C12 O42 SINGLE NONE 21
SRY C22 C32 SINGLE NONE 22
SRY C22 O13 SINGLE BEGINDASH 23
SRY C32 O32 SINGLE BEGINDASH 24
SRY C32 CG2 SINGLE NONE 25
SRY C32 C42 SINGLE NONE 26
SRY CG2 OG2 DOUBLE NONE 27
SRY C42 CH2 SINGLE BEGINDASH 28
SRY C42 O42 SINGLE NONE 29
SRY C13 O13 SINGLE BEGINWEDGE 30
SRY C13 C23 SINGLE NONE 31
SRY C13 O53 SINGLE NONE 32
SRY C23 N23 SINGLE BEGINWEDGE 33
SRY C23 C33 SINGLE NONE 34
SRY N23 CI3 SINGLE NONE 35
SRY C33 O33 SINGLE BEGINDASH 36
SRY C33 C43 SINGLE NONE 37
SRY C43 O43 SINGLE BEGINWEDGE 38
SRY C43 C53 SINGLE NONE 39
SRY C53 O53 SINGLE NONE 40
SRY C53 C63 SINGLE BEGINDASH 41
SRY C63 O63 SINGLE NONE 42
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
SRY MurckoScaffold S1 scaffold 'C1CCC(O[C@@H]2OCC[C@H]2O[C@H]2CCCCO2)CC1' InChI=1S/C15H26O4/c1-2-6-12(7-3-1)18-15-13(9-11-17-15)19-14-8-4-5-10-16-14/h12-15H,1-11H2/t13-,14+,15+/m1/s1 ZVOXSFNMCIUBSV-ILXRZTDVSA-N
SRY cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
SRY furanose F2 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
SRY pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
SRY C11 S1 1
SRY C21 S1 1
SRY C31 S1 1
SRY C41 S1 1
SRY O41 S1 1
SRY C51 S1 1
SRY C61 S1 1
SRY C12 S1 1
SRY C22 S1 1
SRY C32 S1 1
SRY C42 S1 1
SRY O42 S1 1
SRY O13 S1 1
SRY C13 S1 1
SRY C23 S1 1
SRY C33 S1 1
SRY C43 S1 1
SRY C53 S1 1
SRY O53 S1 1
SRY C11 F1 1
SRY C21 F1 1
SRY C31 F1 1
SRY C41 F1 1
SRY C51 F1 1
SRY C61 F1 1
SRY C32 F2 1
SRY C42 F2 1
SRY O42 F2 1
SRY C12 F2 1
SRY C22 F2 1
SRY O41 F2 1
SRY C43 F3 1
SRY C53 F3 1
SRY O53 F3 1
SRY C13 F3 1
SRY C23 F3 1
SRY C33 F3 1
SRY O13 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SRY
_pdbe_chem_comp_rdkit_properties.exactmw 581.266
_pdbe_chem_comp_rdkit_properties.amw 581.580
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 19
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 16
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 14
_pdbe_chem_comp_rdkit_properties.NumHBA 15
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 40
_pdbe_chem_comp_rdkit_properties.NumAtoms 79
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 19
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.857
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 15
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 283.819
_pdbe_chem_comp_rdkit_properties.tpsa 331.430
_pdbe_chem_comp_rdkit_properties.CrippenClogP -7.742
_pdbe_chem_comp_rdkit_properties.CrippenMR 131.399
_pdbe_chem_comp_rdkit_properties.chi0v 18.529
_pdbe_chem_comp_rdkit_properties.chi1v 9.502
_pdbe_chem_comp_rdkit_properties.chi2v 4.469
_pdbe_chem_comp_rdkit_properties.chi3v 4.469
_pdbe_chem_comp_rdkit_properties.chi4v 2.774
_pdbe_chem_comp_rdkit_properties.chi0n 57.529
_pdbe_chem_comp_rdkit_properties.chi1n 27.885
_pdbe_chem_comp_rdkit_properties.chi2n 4.469
_pdbe_chem_comp_rdkit_properties.chi3n 4.469
_pdbe_chem_comp_rdkit_properties.chi4n 2.774
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.270
_pdbe_chem_comp_rdkit_properties.kappa1 8.212
_pdbe_chem_comp_rdkit_properties.kappa2 12.714
_pdbe_chem_comp_rdkit_properties.kappa3 6.003
_pdbe_chem_comp_rdkit_properties.Phi 2.610
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
SRY UniChem DrugBank DB01082
SRY UniChem 'Guide to Pharmacology' 10923
SRY UniChem 'KEGG LIGAND' C00413
SRY UniChem ChEBI 17076
SRY UniChem ZINC ZINC000008214681
SRY UniChem fdasrs Y45QSO73OB
SRY UniChem SureChEMBL SCHEMBL3276
SRY UniChem PharmGKB PA451512
SRY UniChem HMDB HMDB0015214
SRY UniChem NMRShiftDB 60058699
SRY UniChem BindingDb 50103513
SRY UniChem DrugCentral 2481
SRY UniChem MetaboLights MTBLC17076
SRY UniChem BRENDA 2358
SRY UniChem ChemicalBook CB3462887
SRY UniChem DailyMed STREPTOMYCIN
SRY UniChem ClinicalTrials STREPTOMYCIN
SRY UniChem ClinicalTrials 'STREPTOMYCIN SESQUISULFATE'
SRY UniChem ClinicalTrials 'STREPTOMYCIN SULFATE'
SRY UniChem rxnorm STREPTOMYCIN
SRY UniChem rxnorm 'STREPTOMYCIN SULFATE'
SRY UniChem 'Probes And Drugs' PD009818
SRY UniChem 'EPA CompTox Dashboard' DTXSID4023597
SRY UniChem 'PubChem TPHARMA' 14911392
SRY UniChem 'PubChem TPHARMA' 14911393
SRY UniChem PubChem 19649
SRY UniChem ACTor 57-92-1
SRY UniChem Nikkaji J4.500D
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
SRY C11 4.082 -1.989 0.408 ETKDGv3 1
SRY N11 5.223 -1.875 1.333 ETKDGv3 2
SRY CA1 5.451 -0.901 2.377 ETKDGv3 3
SRY NB1 6.741 -0.835 2.986 ETKDGv3 4
SRY NC1 4.527 -0.096 2.801 ETKDGv3 5
SRY C21 3.838 -0.689 -0.393 ETKDGv3 6
SRY O21 4.988 -0.371 -1.136 ETKDGv3 7
SRY C31 2.654 -0.881 -1.370 ETKDGv3 8
SRY N31 2.410 0.317 -2.193 ETKDGv3 9
SRY CD1 2.298 1.690 -1.762 ETKDGv3 10
SRY NE1 2.477 2.732 -2.722 ETKDGv3 11
SRY NF1 1.996 2.017 -0.544 ETKDGv3 12
SRY C41 1.358 -1.397 -0.693 ETKDGv3 13
SRY O41 0.414 -1.675 -1.720 ETKDGv3 14
SRY C51 1.668 -2.703 0.087 ETKDGv3 15
SRY O51 0.517 -3.195 0.727 ETKDGv3 16
SRY C61 2.806 -2.504 1.114 ETKDGv3 17
SRY O61 3.074 -3.736 1.735 ETKDGv3 18
SRY C12 -0.919 -1.376 -1.337 ETKDGv3 19
SRY C22 -1.282 0.060 -1.735 ETKDGv3 20
SRY C32 -1.946 -0.138 -3.090 ETKDGv3 21
SRY O32 -2.936 0.835 -3.337 ETKDGv3 22
SRY CG2 -0.931 -0.120 -4.220 ETKDGv3 23
SRY OG2 -1.298 -0.241 -5.378 ETKDGv3 24
SRY C42 -2.548 -1.548 -2.944 ETKDGv3 25
SRY CH2 -4.012 -1.551 -2.480 ETKDGv3 26
SRY O42 -1.778 -2.273 -2.010 ETKDGv3 27
SRY O13 -2.234 0.603 -0.828 ETKDGv3 28
SRY C13 -1.636 1.254 0.285 ETKDGv3 29
SRY C23 -2.469 2.521 0.682 ETKDGv3 30
SRY N23 -3.807 2.483 0.049 ETKDGv3 31
SRY CI3 -4.306 3.821 -0.279 ETKDGv3 32
SRY C33 -2.551 2.700 2.226 ETKDGv3 33
SRY O33 -1.319 3.211 2.672 ETKDGv3 34
SRY C43 -2.866 1.373 2.978 ETKDGv3 35
SRY O43 -4.159 1.387 3.532 ETKDGv3 36
SRY C53 -2.653 0.140 2.073 ETKDGv3 37
SRY O53 -1.458 0.323 1.344 ETKDGv3 38
SRY C63 -2.540 -1.143 2.908 ETKDGv3 39
SRY O63 -2.408 -2.262 2.073 ETKDGv3 40
SRY H11 4.355 -2.770 -0.341 ETKDGv3 41
SRY HN11 6.007 -2.544 1.159 ETKDGv3 42
SRY HB11 6.933 -0.149 3.750 ETKDGv3 43
SRY HB12 7.510 -1.468 2.675 ETKDGv3 44
SRY HC11 3.550 -0.058 2.452 ETKDGv3 45
SRY H21 3.610 0.139 0.297 ETKDGv3 46
SRY HO21 5.615 0.092 -0.521 ETKDGv3 47
SRY H31 2.968 -1.688 -2.074 ETKDGv3 48
SRY HN31 2.475 0.170 -3.226 ETKDGv3 49
SRY HE11 2.707 2.507 -3.715 ETKDGv3 50
SRY HE12 2.381 3.734 -2.443 ETKDGv3 51
SRY HF11 1.809 1.345 0.225 ETKDGv3 52
SRY H41 0.992 -0.632 0.024 ETKDGv3 53
SRY H51 1.991 -3.476 -0.645 ETKDGv3 54
SRY HO51 0.264 -2.543 1.432 ETKDGv3 55
SRY H61 2.447 -1.778 1.871 ETKDGv3 56
SRY HO61 3.499 -3.534 2.609 ETKDGv3 57
SRY H12 -1.087 -1.532 -0.252 ETKDGv3 58
SRY H22 -0.387 0.713 -1.846 ETKDGv3 59
SRY HO32 -2.490 1.723 -3.318 ETKDGv3 60
SRY HG21 0.127 0.011 -4.019 ETKDGv3 61
SRY H42 -2.519 -2.090 -3.916 ETKDGv3 62
SRY HH21 -4.360 -2.599 -2.354 ETKDGv3 63
SRY HH22 -4.661 -1.063 -3.237 ETKDGv3 64
SRY HH23 -4.123 -1.028 -1.508 ETKDGv3 65
SRY H13 -0.622 1.642 0.048 ETKDGv3 66
SRY H23 -1.911 3.399 0.277 ETKDGv3 67
SRY HN23 -4.505 2.015 0.667 ETKDGv3 68
SRY HI31 -4.371 4.460 0.627 ETKDGv3 69
SRY HI32 -3.646 4.303 -1.031 ETKDGv3 70
SRY HI33 -5.321 3.737 -0.722 ETKDGv3 71
SRY H33 -3.344 3.450 2.454 ETKDGv3 72
SRY HO33 -1.480 3.620 3.563 ETKDGv3 73
SRY H43 -2.158 1.291 3.833 ETKDGv3 74
SRY HO43 -4.813 1.413 2.788 ETKDGv3 75
SRY H53 -3.523 0.004 1.388 ETKDGv3 76
SRY H631 -3.434 -1.261 3.561 ETKDGv3 77
SRY H632 -1.644 -1.087 3.564 ETKDGv3 78
SRY HO63 -3.304 -2.434 1.683 ETKDGv3 79
#