data_JYP
#
_chem_comp.id JYP
_chem_comp.name "Adenophostin A"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H26 N5 O18 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
"[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3-oxidanyl-4,5-diphosphonooxy-oxan-2-yl]oxy-oxolan-3-yl] dihydrogen phosphate"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-10-23
_chem_comp.pdbx_modified_date 2021-03-13
_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 669.322
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code JYP
_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 6MU1
_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
JYP C1 C1 C 0 1 Y N N N N N 181.515 139.482 87.801 7.494 -0.910 -0.448 C1 JYP 1
JYP N1 N1 N 0 1 Y N N N N N 181.775 140.819 87.672 6.304 -0.424 -0.729 N1 JYP 2
JYP C2 C2 C 0 1 Y N N N N N 180.826 141.696 88.010 5.751 0.505 0.045 C2 JYP 3
JYP C3 C3 C 0 1 Y N N N N N 179.573 141.257 88.502 6.457 0.963 1.171 C3 JYP 4
JYP C4 C4 C 0 1 Y N N N N N 179.362 139.924 88.618 7.724 0.414 1.428 C4 JYP 5
JYP N2 N2 N 0 1 Y N N N N N 180.321 139.066 88.286 8.194 -0.511 0.598 N2 JYP 6
JYP N3 N3 N 0 1 N N N N N N 178.142 139.435 89.262 8.466 0.826 2.522 N3 JYP 7
JYP N4 N4 N 0 1 Y N N N N N 178.676 142.512 88.575 5.680 1.893 1.777 N4 JYP 8
JYP C5 C5 C 0 1 Y N N N N N 179.528 143.501 88.124 4.571 2.032 1.111 C5 JYP 9
JYP N5 N5 N 0 1 Y N N N N N 180.663 142.950 87.840 4.567 1.197 0.034 N5 JYP 10
JYP C6 C6 C 0 1 N N R N N N 181.524 143.623 86.892 3.494 1.062 -0.955 C6 JYP 11
JYP C7 C7 C 0 1 N N R N N N 181.540 145.085 87.179 2.513 -0.054 -0.535 C7 JYP 12
JYP C8 C8 C 0 1 N N S N N N 182.915 145.475 87.453 1.128 0.484 -0.958 C8 JYP 13
JYP C9 C9 C 0 1 N N R N N N 183.768 144.256 87.353 1.436 1.863 -1.583 C9 JYP 14
JYP O1 O1 O 0 1 N N N N N N 182.899 143.111 87.018 2.692 2.263 -0.993 O1 JYP 15
JYP C10 C10 C 0 1 N N N N N N 184.450 144.005 88.667 0.337 2.867 -1.228 C10 JYP 16
JYP O2 O2 O 0 1 N N N N N N 185.060 142.723 88.646 0.580 4.099 -1.909 O2 JYP 17
JYP O3 O3 O 0 1 N N N N N N 183.007 146.031 88.801 0.278 0.630 0.182 O3 JYP 18
JYP C11 C11 C 0 1 N N R N N N 182.980 147.455 88.733 -1.112 0.456 -0.103 C11 JYP 19
JYP C12 C12 C 0 1 N N S N N N 184.260 148.010 89.329 -1.939 0.874 1.115 C12 JYP 20
JYP C13 C13 C 0 1 N N R N N N 184.025 148.394 90.807 -3.422 0.628 0.824 C13 JYP 21
JYP C14 C14 C 0 1 N N S N N N 182.985 149.503 90.892 -3.623 -0.847 0.464 C14 JYP 22
JYP C15 C15 C 0 1 N N S N N N 181.929 149.297 89.812 -2.730 -1.200 -0.729 C15 JYP 23
JYP O4 O4 O 0 1 N N N N N N 181.879 147.933 89.449 -1.368 -0.918 -0.402 O4 JYP 24
JYP C16 C16 C 0 1 N N N N N N 180.558 149.730 90.350 -2.880 -2.687 -1.056 C16 JYP 25
JYP O5 O5 O 0 1 N N N N N N 180.272 151.030 89.913 -2.138 -2.991 -2.239 O5 JYP 26
JYP O6 O6 O 0 1 N N N N N N 183.613 150.746 90.701 -4.991 -1.074 0.122 O6 JYP 27
JYP P1 P1 P 0 1 N N N N N N 183.504 151.889 91.921 -5.936 -2.105 0.919 P1 JYP 28
JYP O7 O7 O 0 1 N N N N N N 183.324 151.193 93.249 -7.365 -2.203 0.184 O7 JYP 29
JYP O8 O8 O 0 1 N N N N N N 182.317 152.793 91.662 -5.300 -3.441 0.942 O8 JYP 30
JYP O9 O9 O 0 1 N N N N N N 184.771 152.717 91.953 -6.144 -1.584 2.429 O9 JYP 31
JYP O10 O10 O 0 1 N N N N N N 185.221 148.841 91.364 -3.837 1.447 -0.271 O10 JYP 32
JYP P2 P2 P 0 1 N N N N N N 185.316 148.991 93.006 -5.004 2.550 -0.149 P2 JYP 33
JYP O11 O11 O 0 1 N N N N N N 185.970 147.761 93.586 -5.115 3.370 -1.530 O11 JYP 34
JYP O12 O12 O 0 1 N N N N N N 183.930 149.141 93.580 -6.405 1.817 0.154 O12 JYP 35
JYP O13 O13 O 0 1 N N N N N N 186.139 150.212 93.354 -4.687 3.483 0.955 O13 JYP 36
JYP O14 O14 O 0 1 N N N N N N 184.650 149.142 88.614 -1.729 2.263 1.380 O14 JYP 37
JYP O15 O15 O 0 1 N N N N N N 181.041 145.823 86.018 2.810 -1.269 -1.227 O15 JYP 38
JYP P3 P3 P 0 1 N N N N N N 182.102 146.817 85.186 3.174 -2.642 -0.471 P3 JYP 39
JYP O16 O16 O 0 1 N N N N N N 183.110 147.404 86.151 4.564 -2.466 0.323 O16 JYP 40
JYP O17 O17 O 0 1 N N N N N N 182.825 146.012 84.131 2.098 -2.979 0.487 O17 JYP 41
JYP O18 O18 O 0 1 N N N N N N 181.325 147.940 84.521 3.321 -3.827 -1.552 O18 JYP 42
JYP H1 H1 H 0 1 N N N N N N 182.263 138.757 87.516 7.912 -1.667 -1.096 H1 JYP 43
JYP H2 H2 H 0 1 N N N N N N 178.199 138.443 89.374 8.111 1.502 3.121 H2 JYP 44
JYP H3 H3 H 0 1 N N N N N N 178.042 139.867 90.158 9.340 0.440 2.689 H3 JYP 45
JYP H4 H4 H 0 1 N N N N N N 179.289 144.550 88.026 3.771 2.709 1.373 H4 JYP 46
JYP H5 H5 H 0 1 N N N N N N 181.160 143.456 85.868 3.909 0.852 -1.940 H5 JYP 47
JYP H6 H6 H 0 1 N N N N N N 180.908 145.294 88.055 2.549 -0.210 0.543 H6 JYP 48
JYP H7 H7 H 0 1 N N N N N N 183.250 146.220 86.716 0.669 -0.177 -1.693 H7 JYP 49
JYP H8 H8 H 0 1 N N N N N N 184.524 144.396 86.566 1.534 1.776 -2.665 H8 JYP 50
JYP H9 H9 H 0 1 N N N N N N 185.218 144.774 88.834 -0.631 2.468 -1.531 H9 JYP 51
JYP H10 H10 H 0 1 N N N N N N 183.709 144.045 89.479 0.338 3.040 -0.152 H10 JYP 52
JYP H11 H11 H 0 1 N N N N N N 185.492 142.564 89.477 -0.079 4.784 -1.730 H11 JYP 53
JYP H12 H12 H 0 1 N N N N N N 182.917 147.775 87.683 -1.387 1.072 -0.959 H12 JYP 54
JYP H13 H13 H 0 1 N N N N N N 185.040 147.235 89.287 -1.635 0.287 1.981 H13 JYP 55
JYP H14 H14 H 0 1 N N N N N N 183.650 147.511 91.345 -4.013 0.872 1.707 H14 JYP 56
JYP H15 H15 H 0 1 N N N N N N 182.499 149.462 91.878 -3.353 -1.470 1.317 H15 JYP 57
JYP H16 H16 H 0 1 N N N N N N 182.182 149.919 88.941 -3.027 -0.606 -1.593 H16 JYP 58
JYP H17 H17 H 0 1 N N N N N N 179.785 149.041 89.980 -2.499 -3.282 -0.226 H17 JYP 59
JYP H18 H18 H 0 1 N N N N N N 180.572 149.708 91.450 -3.932 -2.920 -1.217 H18 JYP 60
JYP H19 H19 H 0 1 N N N N N N 179.423 151.297 90.246 -2.187 -3.919 -2.507 H19 JYP 61
JYP H20 H20 H 0 1 N N N N N N 182.504 151.468 93.643 -7.987 -2.807 0.612 H20 JYP 62
JYP H21 H21 H 0 1 N N N N N N 184.557 153.630 91.804 -6.557 -0.712 2.491 H21 JYP 63
JYP H22 H22 H 0 1 N N N N N N 186.762 148.011 94.048 -5.800 4.052 -1.528 H22 JYP 64
JYP H23 H23 H 0 1 N N N N N N 183.865 149.970 94.039 -6.677 1.189 -0.529 H23 JYP 65
JYP H24 H24 H 0 1 N N N N N N 185.452 149.491 88.986 -0.808 2.492 1.569 H24 JYP 66
JYP H25 H25 H 0 1 N N N N N N 183.986 147.144 85.892 5.315 -2.244 -0.244 H25 JYP 67
JYP H26 H26 H 0 1 N N N N N N 181.455 147.902 83.581 3.540 -4.686 -1.166 H26 JYP 68
#
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
JYP O17 P3 DOUB N N 1
JYP O18 P3 SING N N 2
JYP P3 O15 SING N N 3
JYP P3 O16 SING N N 4
JYP O15 C7 SING N N 5
JYP C6 O1 SING N N 6
JYP C6 C7 SING N N 7
JYP C6 N5 SING N N 8
JYP O1 C9 SING N N 9
JYP C7 C8 SING N N 10
JYP C9 C8 SING N N 11
JYP C9 C10 SING N N 12
JYP C8 O3 SING N N 13
JYP N1 C1 DOUB Y N 14
JYP N1 C2 SING Y N 15
JYP C1 N2 SING Y N 16
JYP N5 C2 SING Y N 17
JYP N5 C5 SING Y N 18
JYP C2 C3 DOUB Y N 19
JYP C5 N4 DOUB Y N 20
JYP N2 C4 DOUB Y N 21
JYP C3 N4 SING Y N 22
JYP C3 C4 SING Y N 23
JYP O14 C12 SING N N 24
JYP C4 N3 SING N N 25
JYP O2 C10 SING N N 26
JYP C11 O3 SING N N 27
JYP C11 C12 SING N N 28
JYP C11 O4 SING N N 29
JYP C12 C13 SING N N 30
JYP O4 C15 SING N N 31
JYP C15 C16 SING N N 32
JYP C15 C14 SING N N 33
JYP O5 C16 SING N N 34
JYP O6 C14 SING N N 35
JYP O6 P1 SING N N 36
JYP C13 C14 SING N N 37
JYP C13 O10 SING N N 38
JYP O10 P2 SING N N 39
JYP O8 P1 DOUB N N 40
JYP P1 O9 SING N N 41
JYP P1 O7 SING N N 42
JYP P2 O13 DOUB N N 43
JYP P2 O12 SING N N 44
JYP P2 O11 SING N N 45
JYP C1 H1 SING N N 46
JYP N3 H2 SING N N 47
JYP N3 H3 SING N N 48
JYP C5 H4 SING N N 49
JYP C6 H5 SING N N 50
JYP C7 H6 SING N N 51
JYP C8 H7 SING N N 52
JYP C9 H8 SING N N 53
JYP C10 H9 SING N N 54
JYP C10 H10 SING N N 55
JYP O2 H11 SING N N 56
JYP C11 H12 SING N N 57
JYP C12 H13 SING N N 58
JYP C13 H14 SING N N 59
JYP C14 H15 SING N N 60
JYP C15 H16 SING N N 61
JYP C16 H17 SING N N 62
JYP C16 H18 SING N N 63
JYP O5 H19 SING N N 64
JYP O7 H20 SING N N 65
JYP O9 H21 SING N N 66
JYP O11 H22 SING N N 67
JYP O12 H23 SING N N 68
JYP O14 H24 SING N N 69
JYP O16 H25 SING N N 70
JYP O18 H26 SING N N 71
#
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
JYP InChI InChI 1.03 InChI=1S/C16H26N5O18P3/c17-13-7-14(19-3-18-13)21(4-20-7)15-12(39-42(31,32)33)9(5(1-22)34-15)36-16-8(24)11(38-41(28,29)30)10(6(2-23)35-16)37-40(25,26)27/h3-6,8-12,15-16,22-24H,1-2H2,(H2,17,18,19)(H2,25,26,27)(H2,28,29,30)(H2,31,32,33)/t5-,6+,8+,9+,10+,11-,12-,15-,16-/m1/s1
JYP InChIKey InChI 1.03 RENVITLQVBEFDT-YFPOSXHWSA-N
JYP SMILES_CANONICAL CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H](O[C@H]4O[C@@H](CO)[C@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@@H]4O)[C@H]3O[P](O)(O)=O
JYP SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O[CH]4O[CH](CO)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]4O)[CH]3O[P](O)(O)=O
JYP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]([C@H](O3)CO)O[C@@H]4[C@H]([C@H]([C@H]([C@@H](O4)CO)OP(=O)(O)O)OP(=O)(O)O)O)OP(=O)(O)O)N
JYP SMILES "OpenEye OEToolkits" 2.0.6 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)OC4C(C(C(C(O4)CO)OP(=O)(O)O)OP(=O)(O)O)O)OP(=O)(O)O)N
#
_pdbx_chem_comp_identifier.comp_id JYP
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier
"[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3-oxidanyl-4,5-diphosphonooxy-oxan-2-yl]oxy-oxolan-3-yl] dihydrogen 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
JYP 'Create component' 2018-10-23 RCSB
JYP 'Initial release' 2018-12-05 RCSB
JYP 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id JYP
_pdbx_chem_comp_synonyms.name
"[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3-oxidanyl-4,5-diphosphonooxy-oxan-2-yl]oxy-oxolan-3-yl] dihydrogen phosphate"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id JYP
_pdbe_chem_comp_synonyms.name
'[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3-oxidanyl-4,5-diphosphonooxy-oxan-2-yl]oxy-oxolan-3-yl] dihydrogen phosphate'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
JYP C1 C 11.246 6.701 1
JYP N1 N 11.400 5.209 2
JYP C2 C 12.769 4.597 3
JYP C3 C 13.984 5.476 4
JYP C4 C 13.830 6.968 5
JYP N2 N 12.461 7.581 6
JYP N3 N 15.045 7.848 7
JYP N4 N 15.187 4.595 8
JYP C5 C 14.723 3.178 9
JYP N5 N 13.231 3.179 10
JYP C6 C 12.350 1.965 11
JYP C7 C 12.813 0.539 12
JYP C8 C 11.600 -0.343 13
JYP C9 C 10.386 0.539 14
JYP O1 O 10.850 1.965 15
JYP C10 C 8.960 0.075 16
JYP O2 O 7.845 1.079 17
JYP O3 O 11.600 -1.843 18
JYP C11 C 10.301 -2.593 19
JYP C12 C 10.301 -4.093 20
JYP C13 C 9.002 -4.843 21
JYP C14 C 7.702 -4.093 22
JYP C15 C 7.702 -2.593 23
JYP O4 O 9.002 -1.843 24
JYP C16 C 6.404 -1.843 25
JYP O5 O 6.404 -0.343 26
JYP O6 O 6.404 -4.843 27
JYP P1 P 5.104 -4.093 28
JYP O7 O 5.854 -2.794 29
JYP O8 O 3.805 -3.343 30
JYP O9 O 4.354 -5.392 31
JYP O10 O 9.002 -6.343 32
JYP P2 P 7.702 -7.093 33
JYP O11 O 6.952 -5.794 34
JYP O12 O 8.453 -8.392 35
JYP O13 O 6.404 -7.843 36
JYP O14 O 11.600 -4.843 37
JYP O15 O 14.240 0.075 38
JYP P3 P 14.552 -1.392 39
JYP O16 O 13.084 -1.704 40
JYP O17 O 16.019 -1.080 41
JYP O18 O 14.864 -2.859 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
JYP O17 P3 DOUBLE NONE 1
JYP O18 P3 SINGLE NONE 2
JYP P3 O15 SINGLE NONE 3
JYP P3 O16 SINGLE NONE 4
JYP C7 O15 SINGLE BEGINDASH 5
JYP C6 O1 SINGLE NONE 6
JYP C6 C7 SINGLE NONE 7
JYP C6 N5 SINGLE BEGINWEDGE 8
JYP O1 C9 SINGLE NONE 9
JYP C7 C8 SINGLE NONE 10
JYP C9 C8 SINGLE NONE 11
JYP C9 C10 SINGLE BEGINWEDGE 12
JYP C8 O3 SINGLE BEGINWEDGE 13
JYP N1 C1 DOUBLE NONE 14
JYP N1 C2 SINGLE NONE 15
JYP C1 N2 SINGLE NONE 16
JYP N5 C2 SINGLE NONE 17
JYP N5 C5 SINGLE NONE 18
JYP C2 C3 DOUBLE NONE 19
JYP C5 N4 DOUBLE NONE 20
JYP N2 C4 DOUBLE NONE 21
JYP C3 N4 SINGLE NONE 22
JYP C3 C4 SINGLE NONE 23
JYP C12 O14 SINGLE BEGINWEDGE 24
JYP C4 N3 SINGLE NONE 25
JYP O2 C10 SINGLE NONE 26
JYP C11 O3 SINGLE BEGINDASH 27
JYP C11 C12 SINGLE NONE 28
JYP C11 O4 SINGLE NONE 29
JYP C12 C13 SINGLE NONE 30
JYP O4 C15 SINGLE NONE 31
JYP C15 C16 SINGLE BEGINDASH 32
JYP C15 C14 SINGLE NONE 33
JYP O5 C16 SINGLE NONE 34
JYP C14 O6 SINGLE BEGINWEDGE 35
JYP O6 P1 SINGLE NONE 36
JYP C13 C14 SINGLE NONE 37
JYP C13 O10 SINGLE BEGINWEDGE 38
JYP O10 P2 SINGLE NONE 39
JYP O8 P1 DOUBLE NONE 40
JYP P1 O9 SINGLE NONE 41
JYP P1 O7 SINGLE NONE 42
JYP P2 O13 DOUBLE NONE 43
JYP P2 O12 SINGLE NONE 44
JYP P2 O11 SINGLE NONE 45
#
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
JYP MurckoScaffold S1 scaffold 'c1ncc2ncn([C@H]3C[C@@H](O[C@@H]4CCCCO4)CO3)c2n1' InChI=1S/C14H18N4O3/c1-2-4-19-13(3-1)21-10-5-12(20-7-10)18-9-17-11-6-15-8-16-14(11)18/h6,8-10,12-13H,1-5,7H2/t10-,12-,13-/m1/s1 HLMXDPPFUVPEMO-RAIGVLPGSA-N
JYP adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
JYP imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
JYP 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
JYP purine F4 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
JYP pyranose F5 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
JYP pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
JYP ribose F7 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
JYP C1 S1 1
JYP N1 S1 1
JYP C2 S1 1
JYP C3 S1 1
JYP C4 S1 1
JYP N2 S1 1
JYP N4 S1 1
JYP C5 S1 1
JYP N5 S1 1
JYP C6 S1 1
JYP C7 S1 1
JYP C8 S1 1
JYP C9 S1 1
JYP O1 S1 1
JYP O3 S1 1
JYP C11 S1 1
JYP C12 S1 1
JYP C13 S1 1
JYP C14 S1 1
JYP C15 S1 1
JYP O4 S1 1
JYP N2 F1 1
JYP C4 F1 1
JYP C3 F1 1
JYP C2 F1 1
JYP N1 F1 1
JYP C1 F1 1
JYP N5 F1 1
JYP C5 F1 1
JYP N4 F1 1
JYP N3 F1 1
JYP C2 F2 1
JYP C3 F2 1
JYP N4 F2 1
JYP C5 F2 1
JYP N5 F2 1
JYP O6 F3 1
JYP P1 F3 1
JYP O8 F3 1
JYP O9 F3 1
JYP O7 F3 1
JYP O10 F3 2
JYP P2 F3 2
JYP O13 F3 2
JYP O12 F3 2
JYP O11 F3 2
JYP O15 F3 3
JYP P3 F3 3
JYP O17 F3 3
JYP O18 F3 3
JYP O16 F3 3
JYP N4 F4 1
JYP C5 F4 1
JYP N5 F4 1
JYP C2 F4 1
JYP C3 F4 1
JYP C4 F4 1
JYP N2 F4 1
JYP C1 F4 1
JYP N1 F4 1
JYP C14 F5 1
JYP C15 F5 1
JYP O4 F5 1
JYP C11 F5 1
JYP C12 F5 1
JYP C13 F5 1
JYP O3 F5 1
JYP C3 F6 1
JYP C2 F6 1
JYP N1 F6 1
JYP C1 F6 1
JYP N2 F6 1
JYP C4 F6 1
JYP C7 F7 1
JYP C8 F7 1
JYP C9 F7 1
JYP O1 F7 1
JYP C6 F7 1
JYP C10 F7 1
JYP O2 F7 1
JYP O3 F7 1
JYP O15 F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id JYP
_pdbe_chem_comp_rdkit_properties.exactmw 669.049
_pdbe_chem_comp_rdkit_properties.amw 669.323
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 23
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 11
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 21
_pdbe_chem_comp_rdkit_properties.NumHBD 10
_pdbe_chem_comp_rdkit_properties.NumHBA 23
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 42
_pdbe_chem_comp_rdkit_properties.NumAtoms 68
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 26
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.688
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 9
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 270.437
_pdbe_chem_comp_rdkit_properties.tpsa 358.280
_pdbe_chem_comp_rdkit_properties.CrippenClogP -4.614
_pdbe_chem_comp_rdkit_properties.CrippenMR 125.079
_pdbe_chem_comp_rdkit_properties.chi0v 21.609
_pdbe_chem_comp_rdkit_properties.chi1v 14.008
_pdbe_chem_comp_rdkit_properties.chi2v 5.424
_pdbe_chem_comp_rdkit_properties.chi3v 5.424
_pdbe_chem_comp_rdkit_properties.chi4v 4.024
_pdbe_chem_comp_rdkit_properties.chi0n 44.926
_pdbe_chem_comp_rdkit_properties.chi1n 21.695
_pdbe_chem_comp_rdkit_properties.chi2n 4.206
_pdbe_chem_comp_rdkit_properties.chi3n 4.206
_pdbe_chem_comp_rdkit_properties.chi4n 2.860
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.560
_pdbe_chem_comp_rdkit_properties.kappa1 13.046
_pdbe_chem_comp_rdkit_properties.kappa2 12.442
_pdbe_chem_comp_rdkit_properties.kappa3 7.557
_pdbe_chem_comp_rdkit_properties.Phi 3.865
#
_pdbe_chem_comp_external_mappings.comp_id JYP
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 137349623
#
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
JYP C1 2.028 -0.922 2.969 ETKDGv3 1
JYP N1 2.270 -0.466 1.768 ETKDGv3 2
JYP C2 3.603 -0.560 1.253 ETKDGv3 3
JYP C3 4.581 -1.062 1.956 ETKDGv3 4
JYP C4 4.319 -1.564 3.311 ETKDGv3 5
JYP N2 3.096 -1.490 3.767 ETKDGv3 6
JYP N3 5.362 -2.110 4.117 ETKDGv3 7
JYP N4 5.827 -0.863 1.301 ETKDGv3 8
JYP C5 5.512 -0.241 0.201 ETKDGv3 9
JYP N5 4.104 -0.010 0.046 ETKDGv3 10
JYP C6 3.499 1.036 -0.778 ETKDGv3 11
JYP C7 2.169 0.564 -1.394 ETKDGv3 12
JYP C8 1.166 1.592 -0.901 ETKDGv3 13
JYP C9 2.068 2.742 -0.459 ETKDGv3 14
JYP O1 3.269 2.183 0.007 ETKDGv3 15
JYP C10 1.449 3.636 0.627 ETKDGv3 16
JYP O2 0.213 4.148 0.207 ETKDGv3 17
JYP O3 0.454 1.074 0.214 ETKDGv3 18
JYP C11 -0.852 0.661 -0.143 ETKDGv3 19
JYP C12 -1.598 0.280 1.148 ETKDGv3 20
JYP C13 -3.058 -0.152 0.851 ETKDGv3 21
JYP C14 -3.262 -0.521 -0.640 ETKDGv3 22
JYP C15 -1.977 -1.169 -1.234 ETKDGv3 23
JYP O4 -0.765 -0.442 -1.036 ETKDGv3 24
JYP C16 -1.788 -2.607 -0.729 ETKDGv3 25
JYP O5 -0.700 -3.199 -1.383 ETKDGv3 26
JYP O6 -3.572 0.652 -1.377 ETKDGv3 27
JYP P1 -4.828 0.354 -2.497 ETKDGv3 28
JYP O7 -4.975 1.695 -3.518 ETKDGv3 29
JYP O8 -4.520 -0.869 -3.334 ETKDGv3 30
JYP O9 -6.292 0.136 -1.674 ETKDGv3 31
JYP O10 -3.951 0.896 1.198 ETKDGv3 32
JYP P2 -5.288 0.281 2.066 ETKDGv3 33
JYP O11 -4.768 -0.306 3.565 ETKDGv3 34
JYP O12 -6.403 1.529 2.315 ETKDGv3 35
JYP O13 -5.954 -0.833 1.290 ETKDGv3 36
JYP O14 -1.583 1.357 2.054 ETKDGv3 37
JYP O15 2.230 0.624 -2.807 ETKDGv3 38
JYP P3 2.717 -0.891 -3.425 ETKDGv3 39
JYP O16 1.515 -2.042 -3.114 ETKDGv3 40
JYP O17 2.913 -0.769 -4.919 ETKDGv3 41
JYP O18 4.173 -1.377 -2.711 ETKDGv3 42
JYP H1 1.027 -0.864 3.374 ETKDGv3 43
JYP H2 5.158 -2.459 5.079 ETKDGv3 44
JYP H3 6.339 -2.170 3.754 ETKDGv3 45
JYP H4 6.253 0.088 -0.515 ETKDGv3 46
JYP H5 4.212 1.308 -1.589 ETKDGv3 47
JYP H6 1.871 -0.444 -1.017 ETKDGv3 48
JYP H7 0.503 1.951 -1.727 ETKDGv3 49
JYP H8 2.298 3.383 -1.342 ETKDGv3 50
JYP H9 1.300 3.056 1.562 ETKDGv3 51
JYP H10 2.147 4.471 0.866 ETKDGv3 52
JYP H11 0.410 4.848 -0.469 ETKDGv3 53
JYP H12 -1.390 1.511 -0.622 ETKDGv3 54
JYP H13 -1.063 -0.589 1.602 ETKDGv3 55
JYP H14 -3.221 -1.079 1.455 ETKDGv3 56
JYP H15 -4.088 -1.271 -0.664 ETKDGv3 57
JYP H16 -2.128 -1.244 -2.332 ETKDGv3 58
JYP H17 -2.707 -3.201 -0.938 ETKDGv3 59
JYP H18 -1.606 -2.608 0.367 ETKDGv3 60
JYP H19 -0.620 -4.116 -1.012 ETKDGv3 61
JYP H20 -4.066 1.831 -3.887 ETKDGv3 62
JYP H21 -6.357 -0.839 -1.510 ETKDGv3 63
JYP H22 -5.598 -0.581 4.031 ETKDGv3 64
JYP H23 -6.599 1.876 1.408 ETKDGv3 65
JYP H24 -0.713 1.328 2.531 ETKDGv3 66
JYP H25 1.876 -2.891 -3.473 ETKDGv3 67
JYP H26 4.357 -2.272 -3.092 ETKDGv3 68
#