Structure of PDB 7akr Chain AAA Binding Site BS03

Receptor Information
>7akr Chain AAA (length=344) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSLSRFRGCLAGALLGDCVGSFYAAHDTVDLTSVLRHVQSLEPDPGTPGS
ERTEALYYTDDTAMARALVQSLLAKEAFDEVDMAHRFAQEYKKDPDRGYG
AGVVTVFKKLLNPKCRDVFEPARAQFNGKGSYGNGGAMRVAGISLAYSSV
QDVQKFARLSAQLTHASSLGYNGAILQALAVHLALQGESSSEHFLKQLLG
HMEDLEGDAQSVLDARELGMEERPYSSRLKKIGELLDQASVTREEVVSEL
GNGIAAFESVPTAIYCFLRCMEPDPEIPSAFNSLQRTLIYSISLGGDTDT
IATMAGAIAGAYYGMDQVPESWQQSCEGYEETDILAQSLHRVFQ
Ligand information
Ligand IDAR6
InChIInChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
InChIKeySRNWOUGRCWSEMX-ZQSHOCFMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@H](O4)O)O)O)O)O)N
ACDLabs 12.01O=P(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)(O)OP(=O)(O)OCC4OC(O)C(O)C4O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
FormulaC15 H23 N5 O14 P2
Name[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE;
Adenosine-5-Diphosphoribose
ChEMBL
DrugBankDB02059
ZINCZINC000014880207
PDB chain7akr Chain AAA Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7akr Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		D77 D78 G117 A118 G119 V120 F143 S148 Y149 G150 N151 G152 H182 I271 D314 D316 T317
Binding residue
(residue number reindexed from 1)		D60 D61 G100 A101 G102 V103 F126 S131 Y132 G133 N134 G135 H165 I254 D297 D299 T300
Annotation score5
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:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004649 poly(ADP-ribose) glycohydrolase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0046872 metal ion binding
GO:0061463 O-acetyl-ADP-ribose deacetylase activity
GO:0140292 ADP-ribosylserine hydrolase activity
Biological Process
GO:0006281 DNA repair
GO:0006287 base-excision repair, gap-filling
GO:0060546 negative regulation of necroptotic process
GO:0071451 cellular response to superoxide
GO:0140290 peptidyl-serine ADP-deribosylation
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0016604 nuclear body
GO:0090734 site of DNA damage

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:7akr, PDBe:7akr, PDBj:7akr
PDBsum7akr
PubMed34321462
UniProtQ9NX46|ADPRS_HUMAN ADP-ribosylhydrolase ARH3 (Gene Name=ADPRS)

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