Structure of PDB 6d3a Chain A Binding Site BS01

Receptor Information
>6d3a Chain A (length=347) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGAARSLSRFRGCLAGALLGDCVGSFYEAHVDLTSVLRHVQSLEPDPGTP
GSERTEALYYTDDTAMARALVQSLLAKEAFDEVDMAHRFAQEYKKDPDRG
YGAGVVTVFKKLLNPKCRDVFEPARAQFNGKGSYGNGGAMRVAGISLAYS
SVQDVQKFARLSAQLTHASSLGYNGAILQALAVHLALQGESSSEHFLKQL
LGHMEDLEGDAQSVLDARELGMEERPYSSRLKKIGELLDQASVTREEVVS
ELGNGIAAFESVPTAIYCFLRCMEPDPEIPSAFNSLQRTLIYSISLGGET
DTIATMAGAIAGAYYGMDQVPESWQQSCEGYEETDILAQSLHRVFQK
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 chain6d3a Chain A Residue 401 [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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PDB6d3a Structure of human ADP-ribosyl-acceptor hydrolase 3 bound to ADP-ribose reveals a conformational switch that enables specific substrate recognition.
Resolution1.60001 Å
Binding residue
(original residue number in PDB)		D77 G115 G117 G119 F143 S148 Y149 G150 N151 G152 H182 I271
Binding residue
(residue number reindexed from 1)		D62 G100 G102 G104 F128 S133 Y134 G135 N136 G137 H167 I256
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

View graph for
Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:6d3a, PDBe:6d3a, PDBj:6d3a
PDBsum6d3a
PubMed29907568
UniProtQ9NX46|ADPRS_HUMAN ADP-ribosylhydrolase ARH3 (Gene Name=ADPRS)

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