Structure of PDB 7aqm Chain B Binding Site BS03

Receptor Information
>7aqm Chain B (length=329) Species: 7897 (Latimeria chalumnae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PMVSLAQVRGALCGALLGDCMGAEFEGSDAVELPDVLEFVRLLEKEKKAG
TLFYTDDTAMTRAVIQSLIAKPDFDEVDMAKRFAEEYKKEPTRGYGAGVV
QVFKKLLSPKYSDVFQPAREQFDGKGSYGNGGAMRVASIALAYPNIQDVI
KFARRSAQLTHASPLGYNGAILQALAVHFALQGELKRDTFLEQLIGEMER
IEGKLPFCSRLKKIKEFLASSNVPKADIVDELGHGIAALESVPTAIYSFL
HCMESDPDIPDLYNNLQRTIIYSISLGGDTDTIATMAGAIAGAYYGMDQV
TPSWKRSCEAIVETEESAVKLYELYCKQL
Ligand information
Ligand IDRVK
InChIInChI=1S/C16H25N5O14P2/c1-30-16-12(25)10(23)7(34-16)3-32-37(28,29)35-36(26,27)31-2-6-9(22)11(24)15(33-6)21-5-20-8-13(17)18-4-19-14(8)21/h4-7,9-12,15-16,22-25H,2-3H2,1H3,(H,26,27)(H,28,29)(H2,17,18,19)/t6-,7-,9-,10-,11-,12-,15-,16+/m1/s1
InChIKeyXNNSDOSOBTWHPT-DBXCYWGHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CO[C@@H]1[C@@H]([C@@H]([C@H](O1)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O)O
CACTVS 3.385CO[CH]1O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH](O)[CH]1O
CACTVS 3.385CO[C@H]1O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@@H](O)[C@H]1O
OpenEye OEToolkits 2.0.7COC1C(C(C(O1)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O)O
FormulaC16 H25 N5 O14 P2
NameAdenosine 5'-diphosphoric acid beta-[(3beta,4beta-dihydroxy-5beta-methoxytetrahydrofuran-2alpha-yl)methyl] estere;
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-5-methoxy-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate;
[[(2R,3S,4R,5R)-5-(6-Aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2R,3S,4R,5S)-3,4-dihydroxy-5-methoxyoxolan-2-yl]methyl hydrogen phosphate;
J3.653.949F;
alpha-1''-O-methyl-ADP ribose
ChEMBL
DrugBank
ZINC
PDB chain7aqm Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7aqm Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal.
Resolution2.5 Å
Binding residue
(original residue number in PDB)
E33 D63 G101 G103 G105 V106 F129 S134 Y135 G136 N137 G138 H168 I260 D303 T306
Binding residue
(residue number reindexed from 1)
E26 D56 G94 G96 G98 V99 F122 S127 Y128 G129 N130 G131 H161 I236 D279 T282
Annotation score4
Enzymatic activity
Enzyme Commision number 3.2.1.143: poly(ADP-ribose) glycohydrolase.
3.2.2.-
3.5.1.-
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004649 poly(ADP-ribose) glycohydrolase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0006281 DNA repair
GO:0060546 negative regulation of necroptotic process
GO:0140290 peptidyl-serine ADP-deribosylation
Cellular Component
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:7aqm, PDBe:7aqm, PDBj:7aqm
PDBsum7aqm
PubMed34321462
UniProtH3BCW1|ADPRS_LATCH ADP-ribosylhydrolase ARH3 (Gene Name=adprs)

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