data_GP3
#
_chem_comp.id GP3
_chem_comp.name "DIGUANOSINE-5'-TRIPHOSPHATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H27 N10 O18 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 788.406
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GP3
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1CKO
_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
GP3 N9A AN9 N 0 1 Y N N N N N 44.687 61.859 -3.237 0.224 -0.696 -8.635 N9A GP3 1
GP3 C8A AC8 C 0 1 Y N N N N N 45.326 62.778 -2.439 -0.954 -1.289 -8.287 C8A GP3 2
GP3 N7A AN7 N 0 1 Y N N N N N 44.936 64.034 -2.568 -1.243 -2.230 -9.138 N7A GP3 3
GP3 C5A AC5 C 0 1 Y N N N N N 43.978 63.957 -3.550 -0.270 -2.296 -10.080 C5A GP3 4
GP3 C6A AC6 C 0 1 N N N N N N 43.204 64.964 -4.065 -0.057 -3.105 -11.221 C6A GP3 5
GP3 O6A AO6 O 0 1 N N N N N N 43.279 66.116 -3.709 -0.857 -3.971 -11.531 O6A GP3 6
GP3 N1A AN1 N 0 1 N N N N N N 42.308 64.540 -5.036 1.051 -2.889 -11.962 N1A GP3 7
GP3 C2A AC2 C 0 1 N N N N N N 42.203 63.258 -5.449 1.941 -1.921 -11.603 C2A GP3 8
GP3 N2A AN2 N 0 1 N N N N N N 41.308 62.965 -6.421 3.062 -1.728 -12.372 N2A GP3 9
GP3 N3A AN3 N 0 1 N N N N N N 42.931 62.269 -4.950 1.755 -1.164 -10.546 N3A GP3 10
GP3 C4A AC4 C 0 1 Y N N N N N 43.804 62.672 -3.997 0.677 -1.315 -9.767 C4A GP3 11
GP3 O5D AO5* O 0 1 N N N N N N 46.514 58.176 -6.505 0.413 1.078 -3.750 O5D GP3 12
GP3 C5D AC5* C 0 1 N N N N N N 45.170 58.181 -6.027 0.003 1.996 -4.765 C5D GP3 13
GP3 C4D AC4* C 0 1 N N R N N N 45.083 58.568 -4.632 0.790 1.722 -6.048 C4D GP3 14
GP3 O4D AO4* O 0 1 N N N N N N 45.508 59.904 -4.429 0.522 0.386 -6.526 O4D GP3 15
GP3 C3D AC3* C 0 1 N N S N N N 43.658 58.569 -4.287 0.311 2.651 -7.185 C3D GP3 16
GP3 O3D AO3* O 0 1 N N N N N N 43.158 57.264 -4.015 1.185 3.774 -7.316 O3D GP3 17
GP3 C2D AC2* C 0 1 N N R N N N 43.614 59.375 -3.097 0.375 1.763 -8.450 C2D GP3 18
GP3 O2D AO2* O 0 1 N N N N N N 43.749 58.483 -1.996 1.289 2.312 -9.401 O2D GP3 19
GP3 C1D AC1* C 0 1 N N R N N N 44.883 60.342 -3.236 0.883 0.402 -7.925 C1D GP3 20
GP3 PA PA P 0 1 N N R N N N 47.164 56.795 -6.906 -0.450 1.422 -2.435 PA GP3 21
GP3 O1A O1A O 0 1 N N N N N N 48.126 57.031 -8.005 -0.182 2.817 -2.020 O1A GP3 22
GP3 O2A O2A O 0 1 N N N N N N 47.597 56.082 -5.687 -2.017 1.252 -2.762 O2A GP3 23
GP3 O3A O3A O 0 1 N N N N N N 45.912 56.095 -7.447 -0.038 0.420 -1.245 O3A GP3 24
GP3 PB PB P 0 1 N N N N N N 45.746 54.908 -8.355 -0.935 0.819 0.030 PB GP3 25
GP3 O1B O1B O 0 1 N N N N N N 46.552 55.143 -9.559 -2.368 0.672 -0.307 O1B GP3 26
GP3 O2B O2B O 0 1 N N N N N N 44.272 54.677 -8.491 -0.635 2.347 0.440 O2B GP3 27
GP3 O3B O3B O 0 1 N N N N N N 46.365 53.680 -7.552 -0.573 -0.148 1.265 O3B GP3 28
GP3 PG PG P 0 1 N N R N N N 45.720 52.279 -7.111 -1.501 0.305 2.500 PG GP3 29
GP3 O1G O1G O 0 1 N N N N N N 46.786 51.503 -6.370 -2.926 0.165 2.123 O1G GP3 30
GP3 O2G O2G O 0 1 N N N N N N 45.067 51.613 -8.279 -1.192 1.841 2.868 O2G GP3 31
GP3 O5E BO5* O 0 1 N N N N N N 44.602 52.756 -6.052 -1.190 -0.625 3.776 O5E GP3 32
GP3 C5E BC5* C 0 1 N N N N N N 44.977 53.492 -4.838 -2.041 -0.176 4.832 C5E GP3 33
GP3 C4E BC4* C 0 1 N N R N N N 43.800 54.157 -3.993 -1.793 -1.024 6.082 C4E GP3 34
GP3 O4E BO4* O 0 1 N N N N N N 42.681 53.287 -3.758 -0.432 -0.869 6.516 O4E GP3 35
GP3 C3E BC3* C 0 1 N N S N N N 44.220 54.592 -2.603 -2.701 -0.542 7.230 C3E GP3 36
GP3 O3E BO3* O 0 1 N N N N N N 44.978 55.813 -2.594 -3.567 -1.591 7.666 O3E GP3 37
GP3 C2E BC2* C 0 1 N N R N N N 42.959 54.761 -1.898 -1.708 -0.154 8.357 C2E GP3 38
GP3 O2E BO2* O 0 1 N N N N N N 42.514 56.096 -2.105 -2.194 -0.578 9.632 O2E GP3 39
GP3 C1E BC1* C 0 1 N N R N N N 41.977 53.763 -2.612 -0.438 -0.947 7.957 C1E GP3 40
GP3 N9B BN9 N 0 1 Y N N N N N 41.377 52.677 -1.761 0.762 -0.317 8.513 N9B GP3 41
GP3 C8B BC8 C 0 1 Y N N N N N 40.059 52.368 -1.601 1.473 0.701 7.949 C8B GP3 42
GP3 N7B BN7 N 0 1 Y N N N N N 39.751 51.455 -0.729 2.480 1.012 8.713 N7B GP3 43
GP3 C5B BC5 C 0 1 Y N N N N N 41.005 51.109 -0.228 2.475 0.214 9.808 C5B GP3 44
GP3 C6B BC6 C 0 1 N N N N N N 41.340 50.150 0.786 3.304 0.102 10.949 C6B GP3 45
GP3 O6B BO6 O 0 1 N N N N N N 40.543 49.461 1.439 4.271 0.830 11.092 O6B GP3 46
GP3 N1B BN1 N 0 1 N N N N N N 42.727 50.093 1.033 2.997 -0.832 11.875 N1B GP3 47
GP3 C2B BC2 C 0 1 N N N N N N 43.680 50.845 0.342 1.913 -1.640 11.705 C2B GP3 48
GP3 N2B BN2 N 0 1 N N N N N N 44.981 50.690 0.659 1.626 -2.580 12.663 N2B GP3 49
GP3 N3B BN3 N 0 1 N N N N N N 43.341 51.736 -0.616 1.135 -1.546 10.650 N3B GP3 50
GP3 C4B BC4 C 0 1 Y N N N N N 42.007 51.837 -0.838 1.373 -0.640 9.694 C4B GP3 51
GP3 H8A AH8 H 0 1 N N N N N N 46.122 62.517 -1.721 -1.557 -1.019 -7.432 H8A GP3 52
GP3 H1A AH1 H 0 1 N N N N N N 41.684 65.216 -5.476 1.219 -3.431 -12.749 H1A GP3 53
GP3 H21A AH21 H 0 0 N N N N N N 41.228 61.997 -6.732 3.702 -1.041 -12.132 H21A GP3 54
GP3 H22A AH22 H 0 0 N N N N N N 41.489 63.560 -7.229 3.215 -2.282 -13.154 H22A GP3 55
GP3 H51A AH51 H 0 0 N N N N N N 44.518 58.823 -6.664 0.196 3.016 -4.432 H51A GP3 56
GP3 H52A AH52 H 0 0 N N N N N N 44.676 57.196 -6.203 -1.061 1.873 -4.959 H52A GP3 57
GP3 H4D AH4* H 0 1 N N N N N N 45.713 57.871 -4.031 1.858 1.855 -5.874 H4D GP3 58
GP3 H3D AH3* H 0 1 N N N N N N 43.027 58.950 -5.123 -0.710 2.983 -7.002 H3D GP3 59
GP3 HO3A AHO3 H 0 0 N N N N N N 42.234 57.264 -3.791 0.837 4.317 -8.037 HO3A GP3 60
GP3 H2D AH2* H 0 1 N N N N N N 42.680 59.968 -2.953 -0.614 1.655 -8.892 H2D GP3 61
GP3 HO2A AHO2 H 0 0 N N N N N N 43.719 59.015 -1.209 0.950 3.184 -9.644 HO2A GP3 62
GP3 H1D AH1* H 0 1 N N N N N N 45.477 60.244 -2.297 1.965 0.331 -8.038 H1D GP3 63
GP3 HOA2 2HOA H 0 0 N N N N N N 47.988 55.250 -5.928 -2.148 0.331 -3.028 HOA2 GP3 64
GP3 HOB2 2HOB H 0 0 N N N N N N 44.167 53.927 -9.064 0.306 2.400 0.653 HOB2 GP3 65
GP3 HOG2 2HOG H 0 0 N N N N N N 44.685 50.783 -8.017 -0.256 1.889 3.107 HOG2 GP3 66
GP3 H51B BH51 H 0 0 N N N N N N 45.579 52.828 -4.174 -1.824 0.868 5.054 H51B GP3 67
GP3 H52B BH52 H 0 0 N N N N N N 45.732 54.270 -5.095 -3.082 -0.274 4.527 H52B GP3 68
GP3 H4E BH4* H 0 1 N N N N N N 43.522 55.021 -4.639 -1.996 -2.072 5.864 H4E GP3 69
GP3 H3E BH3* H 0 1 N N N N N N 44.899 53.843 -2.133 -3.282 0.325 6.918 H3E GP3 70
GP3 HO3B BHO3 H 0 0 N N N N N N 45.241 56.085 -1.722 -4.064 -1.248 8.422 HO3B GP3 71
GP3 H2E BH2* H 0 1 N N N N N N 43.030 54.571 -0.801 -1.514 0.918 8.354 H2E GP3 72
GP3 HO2B BHO2 H 0 0 N N N N N N 41.690 56.206 -1.644 -2.981 -0.049 9.821 HO2B GP3 73
GP3 H1E BH1* H 0 1 N N N N N N 41.045 54.307 -2.892 -0.513 -1.983 8.286 H1E GP3 74
GP3 H8B BH8 H 0 1 N N N N N N 39.249 52.852 -2.172 1.237 1.178 7.009 H8B GP3 75
GP3 H1B BH1 H 0 1 N N N N N N 43.064 49.464 1.762 3.551 -0.927 12.666 H1B GP3 76
GP3 H21B BH21 H 0 0 N N N N N N 45.676 51.239 0.154 0.858 -3.163 12.555 H21B GP3 77
GP3 H22B BH22 H 0 0 N N N N N N 45.223 49.701 0.585 2.191 -2.662 13.447 H22B GP3 78
#
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
GP3 N9A C8A SING Y N 1
GP3 N9A C4A SING Y N 2
GP3 N9A C1D SING N N 3
GP3 C8A N7A DOUB Y N 4
GP3 C8A H8A SING N N 5
GP3 N7A C5A SING Y N 6
GP3 C5A C6A SING N N 7
GP3 C5A C4A DOUB Y N 8
GP3 C6A O6A DOUB N N 9
GP3 C6A N1A SING N N 10
GP3 N1A C2A SING N N 11
GP3 N1A H1A SING N N 12
GP3 C2A N2A SING N N 13
GP3 C2A N3A DOUB N N 14
GP3 N2A H21A SING N N 15
GP3 N2A H22A SING N N 16
GP3 N3A C4A SING N N 17
GP3 O5D C5D SING N N 18
GP3 O5D PA SING N N 19
GP3 C5D C4D SING N N 20
GP3 C5D H51A SING N N 21
GP3 C5D H52A SING N N 22
GP3 C4D O4D SING N N 23
GP3 C4D C3D SING N N 24
GP3 C4D H4D SING N N 25
GP3 O4D C1D SING N N 26
GP3 C3D O3D SING N N 27
GP3 C3D C2D SING N N 28
GP3 C3D H3D SING N N 29
GP3 O3D HO3A SING N N 30
GP3 C2D O2D SING N N 31
GP3 C2D C1D SING N N 32
GP3 C2D H2D SING N N 33
GP3 O2D HO2A SING N N 34
GP3 C1D H1D SING N N 35
GP3 PA O1A DOUB N N 36
GP3 PA O2A SING N N 37
GP3 PA O3A SING N N 38
GP3 O2A HOA2 SING N N 39
GP3 O3A PB SING N N 40
GP3 PB O1B DOUB N N 41
GP3 PB O2B SING N N 42
GP3 PB O3B SING N N 43
GP3 O2B HOB2 SING N N 44
GP3 O3B PG SING N N 45
GP3 PG O1G DOUB N N 46
GP3 PG O2G SING N N 47
GP3 PG O5E SING N N 48
GP3 O2G HOG2 SING N N 49
GP3 O5E C5E SING N N 50
GP3 C5E C4E SING N N 51
GP3 C5E H51B SING N N 52
GP3 C5E H52B SING N N 53
GP3 C4E O4E SING N N 54
GP3 C4E C3E SING N N 55
GP3 C4E H4E SING N N 56
GP3 O4E C1E SING N N 57
GP3 C3E O3E SING N N 58
GP3 C3E C2E SING N N 59
GP3 C3E H3E SING N N 60
GP3 O3E HO3B SING N N 61
GP3 C2E O2E SING N N 62
GP3 C2E C1E SING N N 63
GP3 C2E H2E SING N N 64
GP3 O2E HO2B SING N N 65
GP3 C1E N9B SING N N 66
GP3 C1E H1E SING N N 67
GP3 N9B C8B SING Y N 68
GP3 N9B C4B SING Y N 69
GP3 C8B N7B DOUB Y N 70
GP3 C8B H8B SING N N 71
GP3 N7B C5B SING Y N 72
GP3 C5B C6B SING N N 73
GP3 C5B C4B DOUB Y N 74
GP3 C6B O6B DOUB N N 75
GP3 C6B N1B SING N N 76
GP3 N1B C2B SING N N 77
GP3 N1B H1B SING N N 78
GP3 C2B N2B SING N N 79
GP3 C2B N3B DOUB N N 80
GP3 N2B H21B SING N N 81
GP3 N2B H22B SING N N 82
GP3 N3B C4B SING N N 83
#
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
GP3 SMILES_CANONICAL CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)[C@@H](O)[C@H]3O
GP3 SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)[CH](O)[CH]3O
GP3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N=C(NC2=O)N
GP3 SMILES "OpenEye OEToolkits" 1.5.0 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N=C(NC2=O)N
GP3 InChI InChI 1.03 InChI=1S/C20H27N10O18P3/c21-19-25-13-7(15(35)27-19)23-3-29(13)17-11(33)9(31)5(45-17)1-43-49(37,38)47-51(41,42)48-50(39,40)44-2-6-10(32)12(34)18(46-6)30-4-24-8-14(30)26-20(22)28-16(8)36/h3-6,9-12,17-18,31-34H,1-2H2,(H,37,38)(H,39,40)(H,41,42)(H3,21,25,27,35)(H3,22,26,28,36)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
GP3 InChIKey InChI 1.03 AAXYAFFKOSNMEB-MHARETSRSA-N
#
_pdbx_chem_comp_identifier.comp_id GP3
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 1.5.0
_pdbx_chem_comp_identifier.identifier
"[[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl 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
GP3 'Create component' 1999-07-08 RCSB
GP3 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id GP3
_pdbe_chem_comp_drugbank_details.drugbank_id DB03931
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name "Diguanosine-5'-Triphosphate"
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id GP3
_pdbe_chem_comp_synonyms.name "Diguanosine-5'-Triphosphate"
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GP3
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03931
_pdbe_chem_comp_drugbank_classification.parent "(5'->5')-dinucleotides"
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class "(5'->5')-dinucleotides"
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
"This compound belongs to the class of organic compounds known as (5'->5')-dinucleotides. These are dinucleotides where the two bases are connected via a (5'->5')-phosphodiester linkage."
#
_pdbe_chem_comp_drugbank_targets.comp_id GP3
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03931
_pdbe_chem_comp_drugbank_targets.name 'mRNA-capping enzyme'
_pdbe_chem_comp_drugbank_targets.organism PBCV-1
_pdbe_chem_comp_drugbank_targets.uniprot_id Q84424
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
GP3 N9A N 25.681 4.801 1
GP3 C8A C 24.806 6.008 2
GP3 N7A N 25.681 7.215 3
GP3 C5A C 27.101 6.758 4
GP3 C6A C 28.399 7.508 5
GP3 O6A O 28.399 9.008 6
GP3 N1A N 29.698 6.758 7
GP3 C2A C 29.698 5.258 8
GP3 N2A N 30.998 4.508 9
GP3 N3A N 28.399 4.508 10
GP3 C4A C 27.101 5.258 11
GP3 O5D O 21.201 1.147 12
GP3 C5D C 22.570 0.534 13
GP3 C4D C 23.785 1.414 14
GP3 O4D O 23.788 2.914 15
GP3 C3D C 25.211 0.948 16
GP3 O3D O 25.672 -0.479 17
GP3 C2D C 26.095 2.160 18
GP3 O2D O 27.595 2.157 19
GP3 C1D C 25.215 3.375 20
GP3 PA P 19.986 0.267 21
GP3 O1A O 20.865 -0.948 22
GP3 O2A O 19.106 1.482 23
GP3 O3A O 18.771 -0.612 24
GP3 PB P 17.401 0.000 25
GP3 O1B O 18.014 1.369 26
GP3 O2B O 16.789 -1.369 27
GP3 O3B O 16.032 0.612 28
GP3 PG P 14.817 -0.267 29
GP3 O1G O 15.697 -1.482 30
GP3 O2G O 13.938 0.948 31
GP3 O5E O 13.602 -1.147 32
GP3 C5E C 12.233 -0.534 33
GP3 C4E C 11.018 -1.414 34
GP3 O4E O 11.015 -2.914 35
GP3 C3E C 9.592 -0.948 36
GP3 O3E O 9.131 0.479 37
GP3 C2E C 8.708 -2.160 38
GP3 O2E O 7.208 -2.157 39
GP3 C1E C 9.588 -3.375 40
GP3 N9B N 9.122 -4.801 41
GP3 C8B C 9.997 -6.008 42
GP3 N7B N 9.122 -7.215 43
GP3 C5B C 7.702 -6.758 44
GP3 C6B C 6.404 -7.508 45
GP3 O6B O 6.404 -9.008 46
GP3 N1B N 5.104 -6.758 47
GP3 C2B C 5.104 -5.258 48
GP3 N2B N 3.805 -4.508 49
GP3 N3B N 6.404 -4.508 50
GP3 C4B C 7.702 -5.258 51
#
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
GP3 N9A C8A SINGLE NONE 1
GP3 N9A C4A SINGLE NONE 2
GP3 C1D N9A SINGLE BEGINWEDGE 3
GP3 C8A N7A DOUBLE NONE 4
GP3 N7A C5A SINGLE NONE 5
GP3 C5A C6A SINGLE NONE 6
GP3 C5A C4A DOUBLE NONE 7
GP3 C6A O6A DOUBLE NONE 8
GP3 C6A N1A SINGLE NONE 9
GP3 N1A C2A SINGLE NONE 10
GP3 C2A N2A SINGLE NONE 11
GP3 C2A N3A DOUBLE NONE 12
GP3 N3A C4A SINGLE NONE 13
GP3 O5D C5D SINGLE NONE 14
GP3 O5D PA SINGLE NONE 15
GP3 C4D C5D SINGLE BEGINWEDGE 16
GP3 C4D O4D SINGLE NONE 17
GP3 C4D C3D SINGLE NONE 18
GP3 O4D C1D SINGLE NONE 19
GP3 C3D O3D SINGLE BEGINDASH 20
GP3 C3D C2D SINGLE NONE 21
GP3 C2D O2D SINGLE BEGINDASH 22
GP3 C2D C1D SINGLE NONE 23
GP3 PA O1A DOUBLE NONE 24
GP3 PA O2A SINGLE BEGINWEDGE 25
GP3 PA O3A SINGLE NONE 26
GP3 O3A PB SINGLE NONE 27
GP3 PB O1B DOUBLE NONE 28
GP3 PB O2B SINGLE NONE 29
GP3 PB O3B SINGLE NONE 30
GP3 O3B PG SINGLE NONE 31
GP3 PG O1G DOUBLE NONE 32
GP3 PG O2G SINGLE BEGINDASH 33
GP3 PG O5E SINGLE NONE 34
GP3 O5E C5E SINGLE NONE 35
GP3 C4E C5E SINGLE BEGINWEDGE 36
GP3 C4E O4E SINGLE NONE 37
GP3 C4E C3E SINGLE NONE 38
GP3 O4E C1E SINGLE NONE 39
GP3 C3E O3E SINGLE BEGINDASH 40
GP3 C3E C2E SINGLE NONE 41
GP3 C2E O2E SINGLE BEGINDASH 42
GP3 C2E C1E SINGLE NONE 43
GP3 C1E N9B SINGLE BEGINWEDGE 44
GP3 N9B C8B SINGLE NONE 45
GP3 N9B C4B SINGLE NONE 46
GP3 C8B N7B DOUBLE NONE 47
GP3 N7B C5B SINGLE NONE 48
GP3 C5B C6B SINGLE NONE 49
GP3 C5B C4B DOUBLE NONE 50
GP3 C6B O6B DOUBLE NONE 51
GP3 C6B N1B SINGLE NONE 52
GP3 N1B C2B SINGLE NONE 53
GP3 C2B N2B SINGLE NONE 54
GP3 C2B N3B DOUBLE NONE 55
GP3 N3B C4B SINGLE NONE 56
#
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
GP3 MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1ncn2[C@H]1CC[C@@H](CO[PH](=O)O[PH](=O)O[PH](=O)OC[C@@H]2CC[C@H](n3cnc4c(=O)[nH]cnc43)O2)O1' InChI=1S/C20H25N8O11P3/c29-19-15-17(21-7-23-19)27(9-25-15)13-3-1-11(36-13)5-34-40(31)38-42(33)39-41(32)35-6-12-2-4-14(37-12)28-10-26-16-18(28)22-8-24-20(16)30/h7-14,40-42H,1-6H2,(H,21,23,29)(H,22,24,30)/t11-,12-,13+,14+/m0/s1 BJTIJDJBAIRTKU-IGQOVBAYSA-N
GP3 imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
GP3 phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
GP3 purine F3 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
GP3 pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
GP3 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
GP3 N9A S1 1
GP3 C8A S1 1
GP3 N7A S1 1
GP3 C5A S1 1
GP3 C6A S1 1
GP3 O6A S1 1
GP3 N1A S1 1
GP3 C2A S1 1
GP3 N3A S1 1
GP3 C4A S1 1
GP3 O5D S1 1
GP3 C5D S1 1
GP3 C4D S1 1
GP3 O4D S1 1
GP3 C3D S1 1
GP3 C2D S1 1
GP3 C1D S1 1
GP3 PA S1 1
GP3 O1A S1 1
GP3 O3A S1 1
GP3 PB S1 1
GP3 O1B S1 1
GP3 O3B S1 1
GP3 PG S1 1
GP3 O1G S1 1
GP3 O5E S1 1
GP3 C5E S1 1
GP3 C4E S1 1
GP3 O4E S1 1
GP3 C3E S1 1
GP3 C2E S1 1
GP3 C1E S1 1
GP3 N9B S1 1
GP3 C8B S1 1
GP3 N7B S1 1
GP3 C5B S1 1
GP3 C6B S1 1
GP3 O6B S1 1
GP3 N1B S1 1
GP3 C2B S1 1
GP3 N3B S1 1
GP3 C4B S1 1
GP3 C5A F1 1
GP3 C4A F1 1
GP3 N9A F1 1
GP3 C8A F1 1
GP3 N7A F1 1
GP3 C5B F1 2
GP3 C4B F1 2
GP3 N9B F1 2
GP3 C8B F1 2
GP3 N7B F1 2
GP3 O5D F2 1
GP3 PA F2 1
GP3 O1A F2 1
GP3 O2A F2 1
GP3 O3A F2 1
GP3 O3A F2 2
GP3 PB F2 2
GP3 O1B F2 2
GP3 O2B F2 2
GP3 O3B F2 2
GP3 O3B F2 3
GP3 PG F2 3
GP3 O1G F2 3
GP3 O2G F2 3
GP3 O5E F2 3
GP3 N7A F3 1
GP3 C8A F3 1
GP3 N9A F3 1
GP3 C4A F3 1
GP3 C5A F3 1
GP3 C6A F3 1
GP3 N1A F3 1
GP3 C2A F3 1
GP3 N3A F3 1
GP3 N7B F3 2
GP3 C8B F3 2
GP3 N9B F3 2
GP3 C4B F3 2
GP3 C5B F3 2
GP3 C6B F3 2
GP3 N1B F3 2
GP3 C2B F3 2
GP3 N3B F3 2
GP3 C5A F4 1
GP3 C6A F4 1
GP3 N1A F4 1
GP3 C2A F4 1
GP3 N3A F4 1
GP3 C4A F4 1
GP3 C5B F4 2
GP3 C6B F4 2
GP3 N1B F4 2
GP3 C2B F4 2
GP3 N3B F4 2
GP3 C4B F4 2
GP3 C2D F5 1
GP3 C3D F5 1
GP3 C4D F5 1
GP3 O4D F5 1
GP3 C1D F5 1
GP3 C5D F5 1
GP3 O5D F5 1
GP3 O3D F5 1
GP3 O2D F5 1
GP3 C2E F5 2
GP3 C3E F5 2
GP3 C4E F5 2
GP3 O4E F5 2
GP3 C1E F5 2
GP3 C5E F5 2
GP3 O5E F5 2
GP3 O3E F5 2
GP3 O2E F5 2
#
_pdbe_chem_comp_rdkit_properties.comp_id GP3
_pdbe_chem_comp_rdkit_properties.exactmw 788.072
_pdbe_chem_comp_rdkit_properties.amw 788.410
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 28
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 13
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 21
_pdbe_chem_comp_rdkit_properties.NumHBD 11
_pdbe_chem_comp_rdkit_properties.NumHBA 26
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 51
_pdbe_chem_comp_rdkit_properties.NumAtoms 78
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 31
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 6
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 4
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 6
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 4
_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 10
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 318.428
_pdbe_chem_comp_rdkit_properties.tpsa 427.380
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.795
_pdbe_chem_comp_rdkit_properties.CrippenMR 154.675
_pdbe_chem_comp_rdkit_properties.chi0v 25.846
_pdbe_chem_comp_rdkit_properties.chi1v 16.494
_pdbe_chem_comp_rdkit_properties.chi2v 9.338
_pdbe_chem_comp_rdkit_properties.chi3v 9.338
_pdbe_chem_comp_rdkit_properties.chi4v 6.609
_pdbe_chem_comp_rdkit_properties.chi0n 50.162
_pdbe_chem_comp_rdkit_properties.chi1n 24.654
_pdbe_chem_comp_rdkit_properties.chi2n 5.508
_pdbe_chem_comp_rdkit_properties.chi3n 5.508
_pdbe_chem_comp_rdkit_properties.chi4n 3.605
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.530
_pdbe_chem_comp_rdkit_properties.kappa1 16.231
_pdbe_chem_comp_rdkit_properties.kappa2 13.465
_pdbe_chem_comp_rdkit_properties.kappa3 7.530
_pdbe_chem_comp_rdkit_properties.Phi 4.286
#
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
GP3 UniChem DrugBank DB03931
GP3 UniChem ZINC ZINC000085426282
GP3 UniChem HMDB HMDB0001379
GP3 UniChem 'PubChem TPHARMA' 16177245
GP3 UniChem PubChem 135450902
GP3 UniChem ACTor 6674-45-9
GP3 UniChem BRENDA 103917
GP3 UniChem BRENDA 21403
GP3 UniChem BRENDA 44660
GP3 UniChem MedChemExpress HY-139099
GP3 UniChem 'Probes And Drugs' PD059562
GP3 UniChem Nikkaji J398.255F
#
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
GP3 N9A -4.421 1.465 2.501 ETKDGv3 1
GP3 C8A -3.770 1.320 3.772 ETKDGv3 2
GP3 N7A -3.664 0.084 4.168 ETKDGv3 3
GP3 C5A -4.302 -0.665 3.140 ETKDGv3 4
GP3 C6A -4.462 -2.109 3.022 ETKDGv3 5
GP3 O6A -4.023 -2.898 3.898 ETKDGv3 6
GP3 N1A -5.138 -2.593 1.851 ETKDGv3 7
GP3 C2A -5.623 -1.649 0.867 ETKDGv3 8
GP3 N2A -6.282 -2.119 -0.307 ETKDGv3 9
GP3 N3A -5.444 -0.365 1.039 ETKDGv3 10
GP3 C4A -4.764 0.122 2.205 ETKDGv3 11
GP3 O5D -4.153 1.116 -1.483 ETKDGv3 12
GP3 C5D -3.522 2.197 -0.836 ETKDGv3 13
GP3 C4D -4.600 3.146 -0.285 ETKDGv3 14
GP3 O4D -5.433 2.444 0.609 ETKDGv3 15
GP3 C3D -4.001 4.329 0.464 ETKDGv3 16
GP3 O3D -4.887 5.418 0.390 ETKDGv3 17
GP3 C2D -3.908 3.799 1.879 ETKDGv3 18
GP3 O2D -4.175 4.788 2.840 ETKDGv3 19
GP3 C1D -4.971 2.694 1.922 ETKDGv3 20
GP3 PA -3.030 -0.156 -1.645 ETKDGv3 21
GP3 O1A -3.669 -1.252 -2.470 ETKDGv3 22
GP3 O2A -1.640 0.407 -2.434 ETKDGv3 23
GP3 O3A -2.628 -0.723 -0.088 ETKDGv3 24
GP3 PB -1.784 -2.189 -0.261 ETKDGv3 25
GP3 O1B -2.751 -3.275 -0.680 ETKDGv3 26
GP3 O2B -1.133 -2.588 1.250 ETKDGv3 27
GP3 O3B -0.535 -2.008 -1.406 ETKDGv3 28
GP3 PG 0.240 -3.516 -1.590 ETKDGv3 29
GP3 O1G -0.720 -4.517 -2.194 ETKDGv3 30
GP3 O2G 0.789 -4.104 -0.099 ETKDGv3 31
GP3 O5E 1.578 -3.365 -2.639 ETKDGv3 32
GP3 C5E 2.135 -2.081 -2.477 ETKDGv3 33
GP3 C4E 3.477 -2.004 -3.219 ETKDGv3 34
GP3 O4E 3.947 -0.676 -3.188 ETKDGv3 35
GP3 C3E 4.542 -2.903 -2.591 ETKDGv3 36
GP3 O3E 5.434 -3.389 -3.569 ETKDGv3 37
GP3 C2E 5.223 -1.973 -1.613 ETKDGv3 38
GP3 O2E 6.601 -2.224 -1.512 ETKDGv3 39
GP3 C1E 4.957 -0.584 -2.201 ETKDGv3 40
GP3 N9B 4.547 0.355 -1.155 ETKDGv3 41
GP3 C8B 3.657 1.471 -1.311 ETKDGv3 42
GP3 N7B 3.820 2.405 -0.419 ETKDGv3 43
GP3 C5B 4.890 1.929 0.388 ETKDGv3 44
GP3 C6B 5.598 2.615 1.461 ETKDGv3 45
GP3 O6B 5.226 3.740 1.887 ETKDGv3 46
GP3 N1B 6.748 1.953 2.008 ETKDGv3 47
GP3 C2B 7.162 0.679 1.462 ETKDGv3 48
GP3 N2B 8.317 0.022 1.981 ETKDGv3 49
GP3 N3B 6.487 0.127 0.486 ETKDGv3 50
GP3 C4B 5.320 0.773 -0.043 ETKDGv3 51
GP3 H8A -3.401 2.153 4.354 ETKDGv3 52
GP3 H1A -5.271 -3.619 1.710 ETKDGv3 53
GP3 H21A -6.620 -1.446 -1.031 ETKDGv3 54
GP3 H22A -6.420 -3.142 -0.462 ETKDGv3 55
GP3 H51A -2.892 2.748 -1.568 ETKDGv3 56
GP3 H52A -2.882 1.866 0.016 ETKDGv3 57
GP3 H4D -5.211 3.510 -1.140 ETKDGv3 58
GP3 H3D -2.998 4.610 0.063 ETKDGv3 59
GP3 HO3A -4.356 6.233 0.589 ETKDGv3 60
GP3 H2D -2.890 3.370 2.040 ETKDGv3 61
GP3 HO2A -3.366 5.361 2.885 ETKDGv3 62
GP3 H1D -5.840 3.018 2.536 ETKDGv3 63
GP3 HOA2 -1.967 0.758 -3.301 ETKDGv3 64
GP3 HOB2 -0.562 -1.814 1.488 ETKDGv3 65
GP3 HOG2 1.424 -3.419 0.228 ETKDGv3 66
GP3 H51B 2.306 -1.834 -1.404 ETKDGv3 67
GP3 H52B 1.453 -1.321 -2.920 ETKDGv3 68
GP3 H4E 3.306 -2.298 -4.279 ETKDGv3 69
GP3 H3E 4.099 -3.773 -2.059 ETKDGv3 70
GP3 HO3B 5.813 -2.612 -4.059 ETKDGv3 71
GP3 H2E 4.737 -2.070 -0.612 ETKDGv3 72
GP3 HO2B 6.697 -3.053 -0.974 ETKDGv3 73
GP3 H1E 5.876 -0.193 -2.691 ETKDGv3 74
GP3 H8B 2.924 1.547 -2.104 ETKDGv3 75
GP3 H1B 7.289 2.396 2.784 ETKDGv3 76
GP3 H21B 8.625 -0.897 1.591 ETKDGv3 77
GP3 H22B 8.866 0.452 2.758 ETKDGv3 78
#