data_AGS
#
_chem_comp.id AGS
_chem_comp.name "PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H16 N5 O12 P3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE
MONOTHIOPHOSPHATE
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 SAP,ATG
_chem_comp.formula_weight 523.247
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code AGS
_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 1MMG
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
AGS PG PG P 0 1 N N N N N N 19.268 31.770 23.126 -5.637 -2.115 0.586 PG AGS 1
AGS S1G S1G S 0 1 N N N N N N 21.065 32.639 23.413 -7.391 -1.534 0.347 S1G AGS 2
AGS O2G O2G O 0 1 N N N N N N 18.713 31.367 24.546 -5.542 -2.991 1.934 O2G AGS 3
AGS O3G O3G O 0 1 N N N N N N 19.419 30.562 22.220 -5.194 -3.016 -0.672 O3G AGS 4
AGS PB PB P 0 1 N N N N N N 17.866 33.370 21.089 -4.304 0.389 -0.272 PB AGS 5
AGS O1B O1B O 0 1 N N N N N N 18.381 34.736 20.924 -4.199 -0.101 -1.664 O1B AGS 6
AGS O2B O2B O 0 1 N N N N N N 18.364 32.276 20.112 -5.464 1.501 -0.180 O2B AGS 7
AGS O3B O3B O 0 1 N N N N N N 18.173 32.841 22.584 -4.661 -0.841 0.705 O3B AGS 8
AGS PA PA P 0 1 N N N N N N 15.223 32.680 20.323 -1.862 2.050 -0.526 PA AGS 9
AGS O1A O1A O 0 1 N N N N N N 15.301 32.939 18.769 -1.736 1.711 -1.961 O1A AGS 10
AGS O2A O2A O 0 1 N N N N N N 15.270 31.169 20.572 -2.400 3.561 -0.377 O2A AGS 11
AGS O3A O3A O 0 1 N N N N N N 16.296 33.429 21.145 -2.901 1.039 0.176 O3A AGS 12
AGS "O5'" "O5'" O 0 1 N N N N N N 13.895 33.409 20.870 -0.424 1.920 0.185 "O5'" AGS 13
AGS "C5'" "C5'" C 0 1 N N N N N N 13.156 32.787 21.952 0.738 2.612 -0.278 "C5'" AGS 14
AGS "C4'" "C4'" C 0 1 N N R N N N 11.671 32.879 21.645 1.928 2.266 0.620 "C4'" AGS 15
AGS "O4'" "O4'" O 0 1 N N N N N N 11.338 34.239 21.298 2.268 0.878 0.468 "O4'" AGS 16
AGS "C3'" "C3'" C 0 1 N N S N N N 11.203 32.098 20.420 3.160 3.089 0.196 "C3'" AGS 17
AGS "O3'" "O3'" O 0 1 N N N N N N 11.227 30.645 20.593 3.609 3.911 1.276 "O3'" AGS 18
AGS "C2'" "C2'" C 0 1 N N R N N N 9.870 32.845 20.212 4.227 2.023 -0.153 "C2'" AGS 19
AGS "O2'" "O2'" O 0 1 N N N N N N 8.853 32.591 21.205 5.514 2.411 0.331 "O2'" AGS 20
AGS "C1'" "C1'" C 0 1 N N R N N N 10.315 34.261 20.396 3.702 0.778 0.607 "C1'" AGS 21
AGS N9 N9 N 0 1 Y N N N N N 10.700 34.897 19.153 4.195 -0.453 -0.016 N9 AGS 22
AGS C8 C8 C 0 1 Y N N N N N 11.902 35.271 18.665 3.578 -1.161 -1.004 C8 AGS 23
AGS N7 N7 N 0 1 Y N N N N N 11.791 36.062 17.588 4.295 -2.200 -1.321 N7 AGS 24
AGS C5 C5 C 0 1 Y N N N N N 10.424 36.081 17.338 5.414 -2.225 -0.558 C5 AGS 25
AGS C6 C6 C 0 1 Y N N N N N 9.656 36.702 16.326 6.523 -3.083 -0.458 C6 AGS 26
AGS N6 N6 N 0 1 N N N N N N 10.064 37.403 15.377 6.627 -4.202 -1.266 N6 AGS 27
AGS N1 N1 N 0 1 Y N N N N N 8.322 36.453 16.468 7.469 -2.794 0.429 N1 AGS 28
AGS C2 C2 C 0 1 Y N N N N N 7.752 35.743 17.494 7.378 -1.728 1.204 C2 AGS 29
AGS N3 N3 N 0 1 Y N N N N N 8.432 35.156 18.440 6.358 -0.898 1.145 N3 AGS 30
AGS C4 C4 C 0 1 Y N N N N N 9.762 35.345 18.288 5.367 -1.102 0.284 C4 AGS 31
AGS HOG2 HOG2 H 0 0 N N N N N N 19.339 31.619 25.214 -6.105 -3.777 1.933 HOG2 AGS 32
AGS H21 H21 H 0 1 N N N N N N 20.331 30.463 21.973 -4.290 -3.354 -0.615 H21 AGS 33
AGS HOB2 HOB2 H 0 0 N N N N N N 18.977 32.657 19.494 -5.589 1.867 0.706 HOB2 AGS 34
AGS HOA2 HOA2 H 0 0 N N N N N N 15.336 30.713 19.741 -2.507 3.852 0.539 HOA2 AGS 35
AGS "H5'1" "H5'1" H 0 0 N N N N N N 13.450 31.731 22.042 0.956 2.311 -1.302 "H5'1" AGS 36
AGS "H5'2" "H5'2" H 0 0 N N N N N N 13.372 33.309 22.896 0.558 3.687 -0.245 "H5'2" AGS 37
AGS "H4'" "H4'" H 0 1 N N N N N N 11.096 32.555 22.525 1.681 2.476 1.661 "H4'" AGS 38
AGS "H3'" "H3'" H 0 1 N N N N N N 11.865 32.361 19.582 2.929 3.700 -0.677 "H3'" AGS 39
AGS "HO3'" "HO3'" H 0 0 N N N N N N 10.925 30.226 19.796 4.383 4.450 1.064 "HO3'" AGS 40
AGS "H2'" "H2'" H 0 1 N N N N N N 9.494 32.679 19.191 4.257 1.839 -1.227 "H2'" AGS 41
AGS "HO2'" "HO2'" H 0 0 N N N N N N 8.073 33.091 20.995 5.845 3.235 -0.050 "HO2'" AGS 42
AGS "H1'" "H1'" H 0 1 N N N N N N 9.469 34.822 20.820 3.990 0.820 1.657 "H1'" AGS 43
AGS H8 H8 H 0 1 N N N N N N 12.846 34.968 19.093 2.634 -0.898 -1.457 H8 AGS 44
AGS HN61 HN61 H 0 0 N N N N N N 9.287 37.698 14.822 5.930 -4.402 -1.910 HN61 AGS 45
AGS HN62 HN62 H 0 0 N N N N N N 10.541 38.205 15.736 7.398 -4.786 -1.188 HN62 AGS 46
AGS H2 H2 H 0 1 N N N N N N 6.675 35.665 17.520 8.169 -1.531 1.912 H2 AGS 47
#
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
AGS PG S1G DOUB N N 1
AGS PG O2G SING N N 2
AGS PG O3G SING N N 3
AGS PG O3B SING N N 4
AGS PB O1B DOUB N N 5
AGS PB O2B SING N N 6
AGS PB O3B SING N N 7
AGS PB O3A SING N N 8
AGS PA O1A DOUB N N 9
AGS PA O2A SING N N 10
AGS PA O3A SING N N 11
AGS PA "O5'" SING N N 12
AGS "O5'" "C5'" SING N N 13
AGS "C5'" "C4'" SING N N 14
AGS "C4'" "O4'" SING N N 15
AGS "C4'" "C3'" SING N N 16
AGS "O4'" "C1'" SING N N 17
AGS "C3'" "O3'" SING N N 18
AGS "C3'" "C2'" SING N N 19
AGS "C2'" "O2'" SING N N 20
AGS "C2'" "C1'" SING N N 21
AGS "C1'" N9 SING N N 22
AGS N9 C8 SING Y N 23
AGS N9 C4 SING Y N 24
AGS C8 N7 DOUB Y N 25
AGS N7 C5 SING Y N 26
AGS C5 C6 SING Y N 27
AGS C5 C4 DOUB Y N 28
AGS C6 N6 SING N N 29
AGS C6 N1 DOUB Y N 30
AGS N1 C2 SING Y N 31
AGS C2 N3 DOUB Y N 32
AGS N3 C4 SING Y N 33
AGS O2G HOG2 SING N N 34
AGS O3G H21 SING N N 35
AGS O2B HOB2 SING N N 36
AGS O2A HOA2 SING N N 37
AGS "C5'" "H5'1" SING N N 38
AGS "C5'" "H5'2" SING N N 39
AGS "C4'" "H4'" SING N N 40
AGS "C3'" "H3'" SING N N 41
AGS "O3'" "HO3'" SING N N 42
AGS "C2'" "H2'" SING N N 43
AGS "O2'" "HO2'" SING N N 44
AGS "C1'" "H1'" SING N N 45
AGS C8 H8 SING N N 46
AGS N6 HN61 SING N N 47
AGS N6 HN62 SING N N 48
AGS C2 H2 SING N N 49
#
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
AGS SMILES ACDLabs 12.01 O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
AGS InChI InChI 1.03 InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
AGS InChIKey InChI 1.03 NLTUCYMLOPLUHL-KQYNXXCUSA-N
AGS SMILES_CANONICAL CACTVS 3.370 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
AGS SMILES CACTVS 3.370 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
AGS SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
AGS SMILES "OpenEye OEToolkits" 1.7.6 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
#
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
AGS "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-hydroxy{[(S)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]adenosine"
AGS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] bis(oxidanyl)phosphinothioyl 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
AGS 'Create component' 1999-07-08 PDBJ
AGS 'Modify descriptor' 2011-06-04 RCSB
AGS 'Other modification' 2012-02-03 RCSB
AGS 'Other modification' 2013-02-04 RCSB
AGS 'Modify synonyms' 2020-06-05 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 AGS ATP-GAMMA-S ? ?
2 AGS "ADENOSINE 5'-(3-THIOTRIPHOSPHATE)" ? ?
3 AGS "ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE)" ? ?
4 AGS "ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id AGS
_pdbe_chem_comp_drugbank_details.drugbank_id DB02930
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name "Adenosine 5'-[gamma-thio]triphosphate"
_pdbe_chem_comp_drugbank_details.description
'A nucleoside triphosphate analogue that is ATP in which one of the oxygens attached to 3-phosphate group is replaced by sulfur.'
_pdbe_chem_comp_drugbank_details.cas_number 35094-46-3
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
AGS ATP-GAMMA-S wwPDB ?
AGS "ADENOSINE 5'-(3-THIOTRIPHOSPHATE)" wwPDB ?
AGS "ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE)" wwPDB ?
AGS "ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" wwPDB ?
AGS (gamma-S)ATP DrugBank ?
AGS 'Adenosine 5-O-(3-thiotriphophate)' DrugBank ?
AGS "Adenosine 5'-(3-thio)triphosphate" DrugBank ?
AGS "Adenosine 5'-(gamma-thio)triphosphate" DrugBank ?
AGS "adenosine 5'-[gamma-thio]triphosphate" DrugBank ?
AGS "Adenosine 5'-[γ-thio]triphosphate" DrugBank ?
AGS "Adenosine 5'-O-(3-thiotriphosphate)" DrugBank ?
AGS ATP-gamma-S DrugBank ?
AGS ATP-gammaS DrugBank ?
AGS gamma-Thio-ATP DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id AGS
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02930
_pdbe_chem_comp_drugbank_classification.parent 'Purine ribonucleoside diphosphates'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Purine nucleotides'
_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 purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.'
#
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
AGS DB02930 'ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2' Humans Q10588 unknown 1
AGS DB02930 Synapsin-1 Humans P17600 unknown 2
AGS DB02930 'Branched-chain alpha-ketoacid dehydrogenase kinase' Humans O14874 unknown 3
AGS DB02930 '6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1' Humans P16118 unknown 4
AGS DB02930 'Mismatch repair endonuclease PMS2' Humans P54278 unknown 5
AGS DB02930 'Protein RecA' 'Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)' P62219 unknown 6
AGS DB02930 'Protein RecA' 'Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)' P42443 unknown 7
AGS DB02930 'Protein RecA' 'Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)' Q59560 unknown 8
AGS DB02930 'Chloramphenicol 3-O phosphotransferase' 'Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745)' Q56148 unknown 9
AGS DB02930 'Phosphoribosylglycinamide formyltransferase 2' 'Escherichia coli (strain K12)' P33221 unknown 10
AGS DB02930 'ATP-dependent DNA helicase RecQ' 'Escherichia coli (strain K12)' P15043 unknown 11
AGS DB02930 'DNA polymerase III subunit tau' 'Escherichia coli (strain K12)' P06710 unknown 12
AGS DB02930 'Serine/threonine-protein kinase PknB' 'Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)' P9WI81 unknown 13
AGS DB02930 'Cag alpha' 'Helicobacter pylori' Q7BK04 unknown 14
#
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
AGS PG P 8.660 7.728 1
AGS S1G S 8.199 9.155 2
AGS O2G O 10.088 8.189 3
AGS O3G O 7.233 7.267 4
AGS PB P 8.116 5.188 5
AGS O1B O 7.003 6.193 6
AGS O2B O 9.229 4.182 7
AGS O3B O 9.121 6.301 8
AGS PA P 7.571 2.647 9
AGS O1A O 8.998 3.108 10
AGS O2A O 6.144 2.186 11
AGS O3A O 7.110 4.075 12
AGS "O5'" O 8.032 1.220 13
AGS "C5'" C 7.027 0.107 14
AGS "C4'" C 7.487 -1.320 15
AGS "O4'" O 6.604 -2.532 16
AGS "C3'" C 8.913 -1.786 17
AGS "O3'" O 10.129 -0.907 18
AGS "C2'" C 8.911 -3.287 19
AGS "O2'" O 10.123 -4.170 20
AGS "C1'" C 7.483 -3.748 21
AGS N9 N 7.018 -5.173 22
AGS C8 C 7.893 -6.380 23
AGS N7 N 7.018 -7.588 24
AGS C5 C 5.598 -7.130 25
AGS C6 C 4.299 -7.880 26
AGS N6 N 4.299 -9.380 27
AGS N1 N 3.000 -7.130 28
AGS C2 C 3.000 -5.630 29
AGS N3 N 4.299 -4.880 30
AGS C4 C 5.598 -5.630 31
#
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
AGS PG S1G DOUBLE NONE 1
AGS PG O2G SINGLE NONE 2
AGS PG O3G SINGLE NONE 3
AGS PG O3B SINGLE NONE 4
AGS PB O1B DOUBLE NONE 5
AGS PB O2B SINGLE BEGINDASH 6
AGS PB O3B SINGLE NONE 7
AGS PB O3A SINGLE NONE 8
AGS PA O1A DOUBLE NONE 9
AGS PA O2A SINGLE BEGINWEDGE 10
AGS PA O3A SINGLE NONE 11
AGS PA "O5'" SINGLE NONE 12
AGS "O5'" "C5'" SINGLE NONE 13
AGS "C4'" "C5'" SINGLE BEGINDASH 14
AGS "C4'" "O4'" SINGLE NONE 15
AGS "C4'" "C3'" SINGLE NONE 16
AGS "O4'" "C1'" SINGLE NONE 17
AGS "C3'" "O3'" SINGLE BEGINWEDGE 18
AGS "C3'" "C2'" SINGLE NONE 19
AGS "C2'" "O2'" SINGLE BEGINWEDGE 20
AGS "C2'" "C1'" SINGLE NONE 21
AGS "C1'" N9 SINGLE BEGINDASH 22
AGS N9 C8 SINGLE NONE 23
AGS N9 C4 SINGLE NONE 24
AGS C8 N7 DOUBLE NONE 25
AGS N7 C5 SINGLE NONE 26
AGS C5 C6 DOUBLE NONE 27
AGS C5 C4 SINGLE NONE 28
AGS C6 N6 SINGLE NONE 29
AGS C6 N1 SINGLE NONE 30
AGS N1 C2 DOUBLE NONE 31
AGS C2 N3 SINGLE NONE 32
AGS N3 C4 DOUBLE NONE 33
#
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
AGS MurckoScaffold S1 scaffold 'c1ncc2ncn([C@H]3CCCO3)c2n1' InChI=1S/C9H10N4O/c1-2-8(14-3-1)13-6-12-7-4-10-5-11-9(7)13/h4-6,8H,1-3H2/t8-/m1/s1 DAKONNSVCLKUJN-MRVPVSSYSA-N
AGS 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
AGS imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
AGS 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
AGS 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
AGS pyrimidine F5 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
AGS ribose F6 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
AGS "C4'" S1 1
AGS "O4'" S1 1
AGS "C3'" S1 1
AGS "C2'" S1 1
AGS "C1'" S1 1
AGS N9 S1 1
AGS C8 S1 1
AGS N7 S1 1
AGS C5 S1 1
AGS C6 S1 1
AGS N1 S1 1
AGS C2 S1 1
AGS N3 S1 1
AGS C4 S1 1
AGS N1 F1 1
AGS C6 F1 1
AGS C5 F1 1
AGS C4 F1 1
AGS N3 F1 1
AGS C2 F1 1
AGS N9 F1 1
AGS C8 F1 1
AGS N7 F1 1
AGS N6 F1 1
AGS C5 F2 1
AGS C4 F2 1
AGS N9 F2 1
AGS C8 F2 1
AGS N7 F2 1
AGS O2B F3 1
AGS PB F3 1
AGS O1B F3 1
AGS O3B F3 1
AGS O3A F3 1
AGS O2A F3 2
AGS PA F3 2
AGS O1A F3 2
AGS O3A F3 2
AGS "O5'" F3 2
AGS N7 F4 1
AGS C8 F4 1
AGS N9 F4 1
AGS C4 F4 1
AGS C5 F4 1
AGS C6 F4 1
AGS N1 F4 1
AGS C2 F4 1
AGS N3 F4 1
AGS C5 F5 1
AGS C6 F5 1
AGS N1 F5 1
AGS C2 F5 1
AGS N3 F5 1
AGS C4 F5 1
AGS "C2'" F6 1
AGS "C3'" F6 1
AGS "C4'" F6 1
AGS "O4'" F6 1
AGS "C1'" F6 1
AGS "C5'" F6 1
AGS "O5'" F6 1
AGS "O3'" F6 1
AGS "O2'" F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id AGS
_pdbe_chem_comp_rdkit_properties.exactmw 522.973
_pdbe_chem_comp_rdkit_properties.amw 523.250
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 17
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 15
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 18
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 31
_pdbe_chem_comp_rdkit_properties.NumAtoms 47
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 21
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 200.164
_pdbe_chem_comp_rdkit_properties.tpsa 262.060
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.322
_pdbe_chem_comp_rdkit_properties.CrippenMR 99.124
_pdbe_chem_comp_rdkit_properties.chi0v 17.385
_pdbe_chem_comp_rdkit_properties.chi1v 12.425
_pdbe_chem_comp_rdkit_properties.chi2v 6.983
_pdbe_chem_comp_rdkit_properties.chi3v 6.983
_pdbe_chem_comp_rdkit_properties.chi4v 5.258
_pdbe_chem_comp_rdkit_properties.chi0n 29.885
_pdbe_chem_comp_rdkit_properties.chi1n 14.291
_pdbe_chem_comp_rdkit_properties.chi2n 2.868
_pdbe_chem_comp_rdkit_properties.chi3n 2.868
_pdbe_chem_comp_rdkit_properties.chi4n 1.848
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.940
_pdbe_chem_comp_rdkit_properties.kappa1 10.990
_pdbe_chem_comp_rdkit_properties.kappa2 8.776
_pdbe_chem_comp_rdkit_properties.kappa3 5.899
_pdbe_chem_comp_rdkit_properties.Phi 3.111
#
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
AGS UniChem DrugBank DB02930
AGS UniChem 'KEGG LIGAND' C13742
AGS UniChem ChEBI 27575
AGS UniChem ZINC ZINC000008295128
AGS UniChem eMolecules 29936603
AGS UniChem SureChEMBL SCHEMBL20164791
AGS UniChem ACTor 117750-47-7
AGS UniChem BindingDb 50118217
AGS UniChem BRENDA 105434
AGS UniChem BRENDA 11164
AGS UniChem BRENDA 111965
AGS UniChem BRENDA 118216
AGS UniChem BRENDA 16020
AGS UniChem BRENDA 160839
AGS UniChem BRENDA 171911
AGS UniChem BRENDA 1860
AGS UniChem BRENDA 20276
AGS UniChem BRENDA 23521
AGS UniChem BRENDA 259968
AGS UniChem BRENDA 279139
AGS UniChem BRENDA 29705
AGS UniChem BRENDA 30025
AGS UniChem BRENDA 43800
AGS UniChem BRENDA 57033
AGS UniChem BRENDA 7139
AGS UniChem BRENDA 8035
AGS UniChem BRENDA 92281
AGS UniChem BRENDA 92301
AGS UniChem 'Probes And Drugs' PD059757
AGS UniChem Nikkaji J351.688A
AGS UniChem SureChEMBL SCHEMBL77440
AGS UniChem 'PubChem TPHARMA' 15085670
AGS UniChem 'PubChem TPHARMA' 16650318
AGS UniChem 'PubChem TPHARMA' 24421690
AGS UniChem PubChem 440317
#
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
AGS PG 6.969 0.399 0.413 ETKDGv3 1
AGS S1G 8.279 -0.701 0.166 ETKDGv3 2
AGS O2G 6.300 0.789 -1.094 ETKDGv3 3
AGS O3G 7.564 1.803 1.151 ETKDGv3 4
AGS PB 4.436 0.642 1.455 ETKDGv3 5
AGS O1B 3.461 0.081 2.467 ETKDGv3 6
AGS O2B 4.858 2.207 1.947 ETKDGv3 7
AGS O3B 5.818 -0.352 1.416 ETKDGv3 8
AGS PA 3.128 -0.815 -0.485 ETKDGv3 9
AGS O1A 2.622 -0.785 -1.910 ETKDGv3 10
AGS O2A 4.380 -1.954 -0.399 ETKDGv3 11
AGS O3A 3.700 0.738 -0.079 ETKDGv3 12
AGS "O5'" 1.860 -1.287 0.556 ETKDGv3 13
AGS "C5'" 0.827 -0.333 0.460 ETKDGv3 14
AGS "C4'" -0.315 -0.720 1.408 ETKDGv3 15
AGS "O4'" -1.268 0.323 1.428 ETKDGv3 16
AGS "C3'" -1.004 -2.023 0.977 ETKDGv3 17
AGS "O3'" -1.324 -2.824 2.092 ETKDGv3 18
AGS "C2'" -2.237 -1.526 0.260 ETKDGv3 19
AGS "O2'" -3.336 -2.385 0.426 ETKDGv3 20
AGS "C1'" -2.488 -0.180 0.925 ETKDGv3 21
AGS N9 -3.065 0.772 -0.022 ETKDGv3 22
AGS C8 -2.362 1.469 -1.074 ETKDGv3 23
AGS N7 -3.115 1.895 -2.055 ETKDGv3 24
AGS C5 -4.433 1.485 -1.720 ETKDGv3 25
AGS C6 -5.557 1.536 -2.433 ETKDGv3 26
AGS N6 -5.613 2.173 -3.710 ETKDGv3 27
AGS N1 -6.725 0.888 -1.879 ETKDGv3 28
AGS C2 -6.668 0.238 -0.738 ETKDGv3 29
AGS N3 -5.423 0.153 -0.004 ETKDGv3 30
AGS C4 -4.399 0.787 -0.488 ETKDGv3 31
AGS HOG2 6.918 1.458 -1.483 ETKDGv3 32
AGS H21 7.768 1.535 2.083 ETKDGv3 33
AGS HOB2 5.226 2.095 2.860 ETKDGv3 34
AGS HOA2 4.218 -2.450 0.443 ETKDGv3 35
AGS "H5'1" 1.195 0.673 0.763 ETKDGv3 36
AGS "H5'2" 0.429 -0.279 -0.579 ETKDGv3 37
AGS "H4'" 0.110 -0.832 2.431 ETKDGv3 38
AGS "H3'" -0.377 -2.627 0.284 ETKDGv3 39
AGS "HO3'" -1.869 -2.281 2.720 ETKDGv3 40
AGS "H2'" -2.010 -1.386 -0.823 ETKDGv3 41
AGS "HO2'" -3.166 -3.172 -0.154 ETKDGv3 42
AGS "H1'" -3.186 -0.303 1.783 ETKDGv3 43
AGS H8 -1.290 1.610 -1.071 ETKDGv3 44
AGS HN61 -4.773 2.637 -4.121 ETKDGv3 45
AGS HN62 -6.508 2.182 -4.248 ETKDGv3 46
AGS H2 -7.554 -0.244 -0.350 ETKDGv3 47
#