data_2AA
#
_chem_comp.id 2AA
_chem_comp.name
"5'-O-{[({[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]OXY}PHOSPHINATO)OXY]PHOSPHINATO}CYT"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H31 N5 O13 P2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-09-26
_chem_comp.pdbx_modified_date 2012-01-05
_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 679.530
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2AA
_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 ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
2AA C13 C13 C 0 1 N N N N N N 2.248 21.240 37.999 -1.602 5.067 -0.334 C13 2AA 1
2AA N5 N5 N 0 1 N N N N N N 3.362 20.597 37.677 -3.006 4.967 -0.752 N5 2AA 2
2AA C12 C12 C 0 1 N N N N N N 4.363 20.638 38.548 -3.270 5.816 -1.922 C12 2AA 3
2AA C11 C11 C 0 1 Y N N N N N 3.478 19.956 36.484 -3.358 3.643 -1.008 C11 2AA 4
2AA C10 C10 C 0 1 Y N N N N N 3.068 20.645 35.333 -2.696 2.923 -1.980 C10 2AA 5
2AA "C9'" C9* C 0 1 Y N N N N N 3.153 20.065 34.065 -3.039 1.600 -2.243 "C9'" 2AA 6
2AA "C8'" C8* C 0 1 Y N N N N N 3.661 18.778 33.934 -4.035 0.981 -1.551 "C8'" 2AA 7
2AA "C7'" C7* C 0 1 Y N N N N N 4.086 18.071 35.059 -4.734 1.680 -0.552 "C7'" 2AA 8
2AA "C6'" C6* C 0 1 Y N N N N N 4.001 18.648 36.340 -4.390 3.025 -0.270 "C6'" 2AA 9
2AA "C5'" C5* C 0 1 Y N N N N N 4.439 17.896 37.439 -5.085 3.719 0.732 "C5'" 2AA 10
2AA "C4'" C4* C 0 1 Y N N N N N 4.949 16.608 37.264 -6.075 3.091 1.424 "C4'" 2AA 11
2AA "C3'" C3* C 0 1 Y N N N N N 5.037 16.045 35.990 -6.411 1.766 1.153 "C3'" 2AA 12
2AA "C2'" C2* C 0 1 Y N N N N N 4.594 16.782 34.896 -5.766 1.066 0.180 "C2'" 2AA 13
2AA S1 S1 S 0 1 N N N N N N 4.700 16.101 33.298 -6.207 -0.609 -0.147 S1 2AA 14
2AA "O3'" O3* O 0 1 N N N N N N 3.841 14.852 33.201 -7.214 -0.949 0.797 "O3'" 2AA 15
2AA "O4'" O4* O 0 1 N N N N N N 4.235 17.108 32.269 -6.393 -0.708 -1.552 "O4'" 2AA 16
2AA N4 N4 N 0 1 N N N N N N 6.287 15.763 33.067 -4.890 -1.543 0.218 N4 2AA 17
2AA "C1'" C1* C 0 1 N N N N N N 6.709 16.512 31.887 -4.396 -1.607 1.596 "C1'" 2AA 18
2AA C9 C9 C 0 1 N N N N N N 6.313 15.654 30.699 -3.462 -2.809 1.747 C9 2AA 19
2AA "O2'" O2* O 0 1 N N N N N N 7.424 14.852 30.385 -2.300 -2.615 0.938 "O2'" 2AA 20
2AA P2 P2 P 0 1 N N R N N N 7.895 14.937 28.869 -1.102 -3.687 0.853 P2 2AA 21
2AA "O1'" O1* O 0 1 N N N N N N 7.079 15.980 28.175 -0.600 -3.974 2.216 "O1'" 2AA 22
2AA O9 O9 O 0 1 N N N N N N 9.398 14.979 28.763 -1.643 -5.047 0.184 O9 2AA 23
2AA O8 O8 O 0 1 N N N N N N 7.390 13.463 28.448 0.093 -3.086 -0.043 O8 2AA 24
2AA P1 P1 P 0 1 N N S N N N 8.313 12.150 28.637 1.637 -3.486 -0.263 P1 2AA 25
2AA O7 O7 O 0 1 N N N N N N 7.380 11.004 28.818 2.234 -3.880 1.033 O7 2AA 26
2AA O6 O6 O 0 1 N N N N N N 9.341 12.081 27.584 1.730 -4.719 -1.294 O6 2AA 27
2AA O5 O5 O 0 1 N N N N N N 9.088 12.331 30.013 2.439 -2.225 -0.861 O5 2AA 28
2AA C14 C14 C 0 1 N N N N N N 9.509 11.059 30.516 3.852 -2.228 -1.069 C14 2AA 29
2AA C8 C8 C 0 1 N N R N N N 10.183 11.053 31.877 4.286 -0.879 -1.646 C8 2AA 30
2AA O2 O2 O 0 1 N N N N N N 10.406 9.626 32.108 4.083 0.157 -0.672 O2 2AA 31
2AA C7 C7 C 0 1 N N S N N N 11.561 11.696 31.757 5.792 -0.910 -1.975 C7 2AA 32
2AA O4 O4 O 0 1 N N N N N N 11.608 12.855 32.584 6.005 -0.670 -3.367 O4 2AA 33
2AA C6 C6 C 0 1 N N R N N N 12.523 10.675 32.318 6.388 0.241 -1.129 C6 2AA 34
2AA O3 O3 O 0 1 N N N N N N 12.607 10.872 33.732 7.370 0.966 -1.874 O3 2AA 35
2AA C5 C5 C 0 1 N N R N N N 11.836 9.342 32.048 5.142 1.121 -0.854 C5 2AA 36
2AA N3 N3 N 0 1 Y N N N N N 12.260 8.610 30.809 5.330 1.917 0.361 N3 2AA 37
2AA C4 C4 C 0 1 Y N N N N N 11.919 8.994 29.488 5.302 3.278 0.292 C4 2AA 38
2AA C3 C3 C 0 1 Y N N N N N 12.355 8.228 28.400 5.477 4.002 1.422 C3 2AA 39
2AA C2 C2 C 0 1 Y N N N N N 13.119 7.085 28.613 5.685 3.326 2.642 C2 2AA 40
2AA N2 N2 N 0 1 N N N N N N 13.550 6.333 27.601 5.865 4.037 3.806 N2 2AA 41
2AA N1 N1 N 0 1 Y N N N N N 13.452 6.710 29.904 5.705 1.999 2.661 N1 2AA 42
2AA C1 C1 C 0 1 Y N N N N N 13.039 7.459 30.991 5.525 1.300 1.541 C1 2AA 43
2AA O1 O1 O 0 1 N N N N N N 13.360 7.100 32.118 5.543 0.082 1.586 O1 2AA 44
2AA H131 1H13 H 0 0 N N N N N N 1.378 20.632 37.711 -1.354 6.111 -0.141 H131 2AA 45
2AA H132 2H13 H 0 0 N N N N N N 2.215 22.203 37.469 -1.451 4.484 0.574 H132 2AA 46
2AA H133 3H13 H 0 0 N N N N N N 2.227 21.418 39.084 -0.959 4.681 -1.125 H133 2AA 47
2AA H121 1H12 H 0 0 N N N N N N 4.320 19.751 39.198 -2.635 5.502 -2.750 H121 2AA 48
2AA H122 2H12 H 0 0 N N N N N N 4.278 21.547 39.161 -4.317 5.723 -2.210 H122 2AA 49
2AA H123 3H12 H 0 0 N N N N N N 5.321 20.649 38.007 -3.053 6.855 -1.672 H123 2AA 50
2AA H10 H10 H 0 1 N N N N N N 2.677 21.647 35.429 -1.903 3.391 -2.544 H10 2AA 51
2AA "H9'" H9* H 0 1 N N N N N N 2.826 20.612 33.193 -2.508 1.056 -3.010 "H9'" 2AA 52
2AA "H8'" H8* H 0 1 N N N N N N 3.727 18.323 32.957 -4.287 -0.046 -1.769 "H8'" 2AA 53
2AA "H5'" H5* H 0 1 N N N N N N 4.381 18.317 38.432 -4.835 4.746 0.954 "H5'" 2AA 54
2AA "H4'" H4* H 0 1 N N N N N N 5.279 16.042 38.123 -6.609 3.628 2.195 "H4'" 2AA 55
2AA "H3'" H3* H 0 1 N N N N N N 5.442 15.053 35.855 -7.199 1.290 1.717 "H3'" 2AA 56
2AA HN4 HN4 H 0 1 N N N N N N 6.822 16.040 33.865 -4.445 -2.048 -0.481 HN4 2AA 57
2AA "H1'1" 1H1* H 0 0 N N N N N N 7.790 16.715 31.900 -3.851 -0.692 1.829 "H1'1" 2AA 58
2AA "H1'2" 2H1* H 0 0 N N N N N N 6.209 17.491 31.846 -5.238 -1.713 2.279 "H1'2" 2AA 59
2AA H91 1H9 H 0 1 N N N N N N 6.026 16.280 29.841 -3.165 -2.909 2.791 H91 2AA 60
2AA H92 2H9 H 0 1 N N N N N N 5.447 15.025 30.954 -3.980 -3.714 1.429 H92 2AA 61
2AA HO9 HO9 H 0 1 N N N N N N 9.651 14.988 27.847 -1.988 -4.934 -0.712 HO9 2AA 62
2AA HO6 HO6 H 0 1 N N N N N N 8.922 12.066 26.732 1.357 -4.532 -2.166 HO6 2AA 63
2AA H141 1H14 H 0 0 N N N N N N 10.272 10.702 29.809 4.359 -2.397 -0.119 H141 2AA 64
2AA H142 2H14 H 0 0 N N N N N N 8.611 10.429 30.596 4.115 -3.023 -1.767 H142 2AA 65
2AA H8 H8 H 0 1 N N N N N N 9.602 11.575 32.652 3.713 -0.660 -2.547 H8 2AA 66
2AA H7 H7 H 0 1 N N N N N N 11.796 11.981 30.721 6.227 -1.866 -1.682 H7 2AA 67
2AA HO4 HO4 H 0 1 N N N N N N 11.618 12.593 33.497 6.936 -0.679 -3.630 HO4 2AA 68
2AA H6 H6 H 0 1 N N N N N N 13.533 10.735 31.886 6.810 -0.138 -0.199 H6 2AA 69
2AA HO3 HO3 H 0 1 N N N N N N 12.626 10.029 34.169 8.128 0.432 -2.148 HO3 2AA 70
2AA H5 H5 H 0 1 N N N N N N 12.145 8.612 32.811 4.932 1.766 -1.707 H5 2AA 71
2AA H4 H4 H 0 1 N N N N N N 11.322 9.878 29.320 5.141 3.773 -0.654 H4 2AA 72
2AA H3 H3 H 0 1 N N N N N N 12.098 8.525 27.394 5.458 5.082 1.390 H3 2AA 73
2AA HN21 1HN2 H 0 0 N N N N N N 14.102 5.504 27.688 5.850 5.006 3.789 HN21 2AA 74
2AA HN22 2HN2 H 0 0 N N N N N N 13.232 6.731 26.740 6.008 3.569 4.643 HN22 2AA 75
#
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
2AA C13 N5 SING N N 1
2AA C13 H131 SING N N 2
2AA C13 H132 SING N N 3
2AA C13 H133 SING N N 4
2AA N5 C12 SING N N 5
2AA N5 C11 SING N N 6
2AA C12 H121 SING N N 7
2AA C12 H122 SING N N 8
2AA C12 H123 SING N N 9
2AA C11 C10 DOUB Y N 10
2AA C11 "C6'" SING Y N 11
2AA C10 "C9'" SING Y N 12
2AA C10 H10 SING N N 13
2AA "C9'" "C8'" DOUB Y N 14
2AA "C9'" "H9'" SING N N 15
2AA "C8'" "C7'" SING Y N 16
2AA "C8'" "H8'" SING N N 17
2AA "C7'" "C6'" DOUB Y N 18
2AA "C7'" "C2'" SING Y N 19
2AA "C6'" "C5'" SING Y N 20
2AA "C5'" "C4'" DOUB Y N 21
2AA "C5'" "H5'" SING N N 22
2AA "C4'" "C3'" SING Y N 23
2AA "C4'" "H4'" SING N N 24
2AA "C3'" "C2'" DOUB Y N 25
2AA "C3'" "H3'" SING N N 26
2AA "C2'" S1 SING N N 27
2AA S1 "O3'" DOUB N N 28
2AA S1 "O4'" DOUB N N 29
2AA S1 N4 SING N N 30
2AA N4 "C1'" SING N N 31
2AA N4 HN4 SING N N 32
2AA "C1'" C9 SING N N 33
2AA "C1'" "H1'1" SING N N 34
2AA "C1'" "H1'2" SING N N 35
2AA C9 "O2'" SING N N 36
2AA C9 H91 SING N N 37
2AA C9 H92 SING N N 38
2AA "O2'" P2 SING N N 39
2AA P2 "O1'" DOUB N N 40
2AA P2 O9 SING N N 41
2AA P2 O8 SING N N 42
2AA O9 HO9 SING N N 43
2AA O8 P1 SING N N 44
2AA P1 O7 DOUB N N 45
2AA P1 O6 SING N N 46
2AA P1 O5 SING N N 47
2AA O6 HO6 SING N N 48
2AA O5 C14 SING N N 49
2AA C14 C8 SING N N 50
2AA C14 H141 SING N N 51
2AA C14 H142 SING N N 52
2AA C8 O2 SING N N 53
2AA C8 C7 SING N N 54
2AA C8 H8 SING N N 55
2AA O2 C5 SING N N 56
2AA C7 O4 SING N N 57
2AA C7 C6 SING N N 58
2AA C7 H7 SING N N 59
2AA O4 HO4 SING N N 60
2AA C6 O3 SING N N 61
2AA C6 C5 SING N N 62
2AA C6 H6 SING N N 63
2AA O3 HO3 SING N N 64
2AA C5 N3 SING N N 65
2AA C5 H5 SING N N 66
2AA N3 C4 SING Y N 67
2AA N3 C1 SING Y N 68
2AA C4 C3 DOUB Y N 69
2AA C4 H4 SING N N 70
2AA C3 C2 SING Y N 71
2AA C3 H3 SING N N 72
2AA C2 N2 SING N N 73
2AA C2 N1 DOUB Y N 74
2AA N2 HN21 SING N N 75
2AA N2 HN22 SING N N 76
2AA N1 C1 SING Y N 77
2AA C1 O1 DOUB N N 78
#
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
2AA SMILES ACDLabs 10.04 O=S(=O)(c2c1cccc(N(C)C)c1ccc2)NCCOP(=O)(O)OP(=O)(O)OCC4OC(N3C(=O)N=C(N)C=C3)C(O)C4O
2AA InChI InChI 1.03 InChI=1S/C23H31N5O13P2S/c1-27(2)16-7-3-6-15-14(16)5-4-8-18(15)44(36,37)25-10-12-38-42(32,33)41-43(34,35)39-13-17-20(29)21(30)22(40-17)28-11-9-19(24)26-23(28)31/h3-9,11,17,20-22,25,29-30H,10,12-13H2,1-2H3,(H,32,33)(H,34,35)(H2,24,26,31)/t17-,20-,21-,22-/m1/s1
2AA InChIKey InChI 1.03 OXPWLEWKRGQJQO-BRKWEVRTSA-N
2AA SMILES_CANONICAL CACTVS 3.385 CN(C)c1cccc2c1cccc2[S](=O)(=O)NCCO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)N4C=CC(=NC4=O)N
2AA SMILES CACTVS 3.385 CN(C)c1cccc2c1cccc2[S](=O)(=O)NCCO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)N4C=CC(=NC4=O)N
2AA SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 CN(C)c1cccc2c1cccc2S(=O)(=O)NCCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=NC4=O)N)O)O
2AA SMILES "OpenEye OEToolkits" 1.7.5 CN(C)c1cccc2c1cccc2S(=O)(=O)NCCOP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=NC4=O)N)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
2AA "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(S)-{[(R)-[2-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
2AA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 2-[(5-dimethylaminonaphthalen-1-yl)sulfonylamino]ethyl hydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
2AA 'Create component' 2005-09-26 RCSB
2AA 'Modify descriptor' 2011-06-04 RCSB
2AA 'Modify descriptor' 2012-01-05 RCSB
2AA 'Modify coordinates' 2012-01-05 RCSB
#
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
2AA C13 C 18.397 13.052 1
2AA N5 N 17.107 12.287 2
2AA C12 C 15.800 13.022 3
2AA C11 C 17.124 10.787 4
2AA C10 C 18.484 10.016 5
2AA "C9'" C 18.484 8.454 6
2AA "C8'" C 17.124 7.683 7
2AA "C7'" C 15.784 8.485 8
2AA "C6'" C 15.784 9.985 9
2AA "C5'" C 14.485 10.735 10
2AA "C4'" C 13.185 9.985 11
2AA "C3'" C 13.185 8.485 12
2AA "C2'" C 14.485 7.735 13
2AA S1 S 14.485 6.235 14
2AA "O3'" O 12.985 6.235 15
2AA "O4'" O 15.985 6.235 16
2AA N4 N 14.485 4.735 17
2AA "C1'" C 13.185 3.985 18
2AA C9 C 13.185 2.485 19
2AA "O2'" O 11.886 1.735 20
2AA P2 P 11.886 0.235 21
2AA "O1'" O 10.386 0.235 22
2AA O9 O 13.386 0.235 23
2AA O8 O 11.886 -1.265 24
2AA P1 P 10.588 -2.015 25
2AA O7 O 11.338 -3.314 26
2AA O6 O 9.838 -0.716 27
2AA O5 O 9.288 -2.765 28
2AA C14 C 9.288 -4.265 29
2AA C8 C 7.989 -5.015 30
2AA O2 O 7.833 -6.506 31
2AA C7 C 6.619 -4.405 32
2AA O4 O 6.307 -2.938 33
2AA C6 C 5.615 -5.519 34
2AA O3 O 4.123 -5.363 35
2AA C5 C 6.365 -6.818 36
2AA N3 N 5.755 -8.189 37
2AA C4 C 6.637 -9.402 38
2AA C3 C 6.027 -10.773 39
2AA C2 C 4.535 -10.929 40
2AA N2 N 3.925 -12.300 41
2AA N1 N 3.653 -9.716 42
2AA C1 C 4.263 -8.345 43
2AA O1 O 3.382 -7.132 44
#
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
2AA C13 N5 SINGLE NONE 1
2AA N5 C12 SINGLE NONE 2
2AA N5 C11 SINGLE NONE 3
2AA C11 C10 DOUBLE NONE 4
2AA C11 "C6'" SINGLE NONE 5
2AA C10 "C9'" SINGLE NONE 6
2AA "C9'" "C8'" DOUBLE NONE 7
2AA "C8'" "C7'" SINGLE NONE 8
2AA "C7'" "C6'" DOUBLE NONE 9
2AA "C7'" "C2'" SINGLE NONE 10
2AA "C6'" "C5'" SINGLE NONE 11
2AA "C5'" "C4'" DOUBLE NONE 12
2AA "C4'" "C3'" SINGLE NONE 13
2AA "C3'" "C2'" DOUBLE NONE 14
2AA "C2'" S1 SINGLE NONE 15
2AA S1 "O3'" DOUBLE NONE 16
2AA S1 "O4'" DOUBLE NONE 17
2AA S1 N4 SINGLE NONE 18
2AA N4 "C1'" SINGLE NONE 19
2AA "C1'" C9 SINGLE NONE 20
2AA C9 "O2'" SINGLE NONE 21
2AA "O2'" P2 SINGLE NONE 22
2AA P2 "O1'" DOUBLE NONE 23
2AA P2 O9 SINGLE BEGINDASH 24
2AA P2 O8 SINGLE NONE 25
2AA O8 P1 SINGLE NONE 26
2AA P1 O7 DOUBLE NONE 27
2AA P1 O6 SINGLE BEGINWEDGE 28
2AA P1 O5 SINGLE NONE 29
2AA O5 C14 SINGLE NONE 30
2AA C8 C14 SINGLE BEGINWEDGE 31
2AA C8 O2 SINGLE NONE 32
2AA C8 C7 SINGLE NONE 33
2AA O2 C5 SINGLE NONE 34
2AA C7 O4 SINGLE BEGINDASH 35
2AA C7 C6 SINGLE NONE 36
2AA C6 O3 SINGLE BEGINDASH 37
2AA C6 C5 SINGLE NONE 38
2AA C5 N3 SINGLE BEGINWEDGE 39
2AA N3 C4 SINGLE NONE 40
2AA N3 C1 SINGLE NONE 41
2AA C4 C3 DOUBLE NONE 42
2AA C3 C2 SINGLE NONE 43
2AA C2 N2 SINGLE NONE 44
2AA C2 N1 DOUBLE NONE 45
2AA N1 C1 SINGLE NONE 46
2AA C1 O1 DOUBLE NONE 47
#
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
2AA MurckoScaffold S1 scaffold 'O=c1ncccn1[C@H]1CC[C@@H](CO[PH](=O)O[PH](=O)OCCNS(=O)(=O)c2cccc3ccccc23)O1' InChI=1S/C21H25N3O9P2S/c25-21-22-11-4-13-24(21)20-10-9-17(32-20)15-31-35(27)33-34(26)30-14-12-23-36(28,29)19-8-3-6-16-5-1-2-7-18(16)19/h1-8,11,13,17,20,23,34-35H,9-10,12,14-15H2/t17-,20+/m0/s1 ZSRYMSQXHBABJM-FXAWDEMLSA-N
2AA napthalene F1 fragment c1ccc2ccccc2c1 InChI=1S/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H UFWIBTONFRDIAS-UHFFFAOYSA-N
2AA phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
2AA phosphate F3 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
2AA pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
2AA ribose F5 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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
2AA C11 S1 1
2AA C10 S1 1
2AA "C9'" S1 1
2AA "C8'" S1 1
2AA "C7'" S1 1
2AA "C6'" S1 1
2AA "C5'" S1 1
2AA "C4'" S1 1
2AA "C3'" S1 1
2AA "C2'" S1 1
2AA S1 S1 1
2AA "O3'" S1 1
2AA "O4'" S1 1
2AA N4 S1 1
2AA "C1'" S1 1
2AA C9 S1 1
2AA "O2'" S1 1
2AA P2 S1 1
2AA "O1'" S1 1
2AA O8 S1 1
2AA P1 S1 1
2AA O7 S1 1
2AA O5 S1 1
2AA C14 S1 1
2AA C8 S1 1
2AA O2 S1 1
2AA C7 S1 1
2AA C6 S1 1
2AA C5 S1 1
2AA N3 S1 1
2AA C4 S1 1
2AA C3 S1 1
2AA C2 S1 1
2AA N1 S1 1
2AA C1 S1 1
2AA O1 S1 1
2AA C10 F1 1
2AA "C9'" F1 1
2AA "C8'" F1 1
2AA "C7'" F1 1
2AA "C6'" F1 1
2AA C11 F1 1
2AA "C5'" F1 1
2AA "C4'" F1 1
2AA "C3'" F1 1
2AA "C2'" F1 1
2AA C11 F2 1
2AA C10 F2 1
2AA "C9'" F2 1
2AA "C8'" F2 1
2AA "C7'" F2 1
2AA "C6'" F2 1
2AA "C7'" F2 2
2AA "C6'" F2 2
2AA "C5'" F2 2
2AA "C4'" F2 2
2AA "C3'" F2 2
2AA "C2'" F2 2
2AA "O2'" F3 1
2AA P2 F3 1
2AA "O1'" F3 1
2AA O9 F3 1
2AA O8 F3 1
2AA O8 F3 2
2AA P1 F3 2
2AA O7 F3 2
2AA O6 F3 2
2AA O5 F3 2
2AA C3 F4 1
2AA C4 F4 1
2AA N3 F4 1
2AA C1 F4 1
2AA N1 F4 1
2AA C2 F4 1
2AA C6 F5 1
2AA C7 F5 1
2AA C8 F5 1
2AA O2 F5 1
2AA C5 F5 1
2AA C14 F5 1
2AA O5 F5 1
2AA O4 F5 1
2AA O3 F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 2AA
_pdbe_chem_comp_rdkit_properties.exactmw 679.111
_pdbe_chem_comp_rdkit_properties.amw 679.538
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 18
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 7
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 20
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 17
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 44
_pdbe_chem_comp_rdkit_properties.NumAtoms 75
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 21
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.391
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 294.475
_pdbe_chem_comp_rdkit_properties.tpsa 262.300
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.505
_pdbe_chem_comp_rdkit_properties.CrippenMR 151.760
_pdbe_chem_comp_rdkit_properties.chi0v 22.951
_pdbe_chem_comp_rdkit_properties.chi1v 14.707
_pdbe_chem_comp_rdkit_properties.chi2v 7.811
_pdbe_chem_comp_rdkit_properties.chi3v 7.811
_pdbe_chem_comp_rdkit_properties.chi4v 5.214
_pdbe_chem_comp_rdkit_properties.chi0n 51.346
_pdbe_chem_comp_rdkit_properties.chi1n 25.320
_pdbe_chem_comp_rdkit_properties.chi2n 4.427
_pdbe_chem_comp_rdkit_properties.chi3n 4.427
_pdbe_chem_comp_rdkit_properties.chi4n 2.780
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.770
_pdbe_chem_comp_rdkit_properties.kappa1 11.790
_pdbe_chem_comp_rdkit_properties.kappa2 13.300
_pdbe_chem_comp_rdkit_properties.kappa3 7.893
_pdbe_chem_comp_rdkit_properties.Phi 3.564
#
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
2AA UniChem ZINC ZINC000058633195
2AA UniChem PubChem 6102719
2AA UniChem Nikkaji J2.295.861E
#
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
2AA C13 -9.093 -3.259 -1.738 ETKDGv3 1
2AA N5 -9.522 -1.952 -1.239 ETKDGv3 2
2AA C12 -10.932 -1.705 -0.947 ETKDGv3 3
2AA C11 -8.575 -0.879 -1.126 ETKDGv3 4
2AA C10 -8.604 0.126 -2.013 ETKDGv3 5
2AA "C9'" -7.616 1.213 -1.939 ETKDGv3 6
2AA "C8'" -6.677 1.209 -0.988 ETKDGv3 7
2AA "C7'" -6.621 0.113 0.018 ETKDGv3 8
2AA "C6'" -7.542 -0.884 -0.049 ETKDGv3 9
2AA "C5'" -7.529 -1.965 0.967 ETKDGv3 10
2AA "C4'" -6.603 -1.978 1.926 ETKDGv3 11
2AA "C3'" -5.585 -0.917 1.990 ETKDGv3 12
2AA "C2'" -5.581 0.089 1.099 ETKDGv3 13
2AA S1 -4.312 1.324 1.213 ETKDGv3 14
2AA "O3'" -4.937 2.691 1.200 ETKDGv3 15
2AA "O4'" -3.558 1.175 2.505 ETKDGv3 16
2AA N4 -3.191 1.181 -0.109 ETKDGv3 17
2AA "C1'" -2.651 -0.180 -0.155 ETKDGv3 18
2AA C9 -1.545 -0.272 -1.202 ETKDGv3 19
2AA "O2'" -0.504 0.612 -0.858 ETKDGv3 20
2AA P2 0.724 0.489 -2.037 ETKDGv3 21
2AA "O1'" 1.270 -0.922 -2.080 ETKDGv3 22
2AA O9 0.086 0.879 -3.556 ETKDGv3 23
2AA O8 1.989 1.575 -1.696 ETKDGv3 24
2AA P1 2.374 1.420 -0.043 ETKDGv3 25
2AA O7 1.310 2.104 0.787 ETKDGv3 26
2AA O6 2.478 -0.208 0.417 ETKDGv3 27
2AA O5 3.866 2.185 0.260 ETKDGv3 28
2AA C14 4.844 1.582 -0.555 ETKDGv3 29
2AA C8 6.207 2.209 -0.248 ETKDGv3 30
2AA O2 6.540 1.994 1.103 ETKDGv3 31
2AA C7 7.316 1.616 -1.108 ETKDGv3 32
2AA O4 7.443 2.295 -2.331 ETKDGv3 33
2AA C6 8.535 1.798 -0.235 ETKDGv3 34
2AA O3 9.183 3.015 -0.512 ETKDGv3 35
2AA C5 7.944 1.842 1.178 ETKDGv3 36
2AA N3 8.279 0.614 1.917 ETKDGv3 37
2AA C4 7.512 -0.591 1.729 ETKDGv3 38
2AA C3 7.862 -1.723 2.346 ETKDGv3 39
2AA C2 9.053 -1.760 3.222 ETKDGv3 40
2AA N2 9.412 -2.972 3.884 ETKDGv3 41
2AA N1 9.783 -0.697 3.388 ETKDGv3 42
2AA C1 9.458 0.538 2.741 ETKDGv3 43
2AA O1 10.207 1.539 2.898 ETKDGv3 44
2AA H131 -9.413 -4.054 -1.032 ETKDGv3 45
2AA H132 -9.551 -3.446 -2.732 ETKDGv3 46
2AA H133 -7.988 -3.302 -1.842 ETKDGv3 47
2AA H121 -11.041 -1.377 0.109 ETKDGv3 48
2AA H122 -11.536 -2.626 -1.095 ETKDGv3 49
2AA H123 -11.327 -0.913 -1.618 ETKDGv3 50
2AA H10 -9.342 0.136 -2.806 ETKDGv3 51
2AA "H9'" -7.650 2.016 -2.664 ETKDGv3 52
2AA "H8'" -5.970 2.024 -0.971 ETKDGv3 53
2AA "H5'" -8.274 -2.749 0.947 ETKDGv3 54
2AA "H4'" -6.598 -2.771 2.664 ETKDGv3 55
2AA "H3'" -4.839 -0.973 2.771 ETKDGv3 56
2AA HN4 -3.723 1.350 -0.993 ETKDGv3 57
2AA "H1'1" -3.453 -0.906 -0.414 ETKDGv3 58
2AA "H1'2" -2.224 -0.458 0.834 ETKDGv3 59
2AA H91 -1.179 -1.324 -1.219 ETKDGv3 60
2AA H92 -1.977 -0.015 -2.196 ETKDGv3 61
2AA HO9 0.862 0.853 -4.170 ETKDGv3 62
2AA HO6 2.786 -0.186 1.358 ETKDGv3 63
2AA H141 4.904 0.487 -0.358 ETKDGv3 64
2AA H142 4.610 1.755 -1.630 ETKDGv3 65
2AA H8 6.144 3.308 -0.424 ETKDGv3 66
2AA H7 7.156 0.525 -1.277 ETKDGv3 67
2AA HO4 6.728 1.945 -2.924 ETKDGv3 68
2AA H6 9.242 0.942 -0.358 ETKDGv3 69
2AA HO3 9.810 2.841 -1.262 ETKDGv3 70
2AA H5 8.341 2.724 1.730 ETKDGv3 71
2AA H4 6.643 -0.593 1.084 ETKDGv3 72
2AA H3 7.272 -2.619 2.198 ETKDGv3 73
2AA HN21 8.839 -3.837 3.761 ETKDGv3 74
2AA HN22 10.253 -3.009 4.502 ETKDGv3 75
#