Structure of PDB 4na0 Chain A Binding Site BS01

Receptor Information
>4na0 Chain A (length=501) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKWLGTPIEEMRKMPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPT
HYKDLWDNKHVKMPCSEQNLYAGSRWELIQTALLNKFTRPQNLKDAILKY
NVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQ
PIPLLKQKMNHSVTMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDIN
FNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWER
CEKPLTRLHVTYEGTIEGNGRGMLQVDFANRFVGGGVTGAGLVQEEIRFL
INPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSE
KDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSE
NLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRD
IYSMHTFLTERKLDVGKVYKLLLRYYNEECRNCPGPDIKLYPFIYHAVES
S
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 chain4na0 Chain A Residue 1003 [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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PDB4na0 Crystallographic and biochemical analysis of the mouse poly(ADP-ribose) glycohydrolase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
T718 I719 E720 F731 N733 V746 Q747 E749 Y788 N862 G864 G866 A867 F868 F895
Binding residue
(residue number reindexed from 1)
T265 I266 E267 F278 N280 V293 Q294 E296 Y335 N409 G411 G413 A414 F415 F442
Annotation score5
Enzymatic activity
Enzyme Commision number 3.2.1.143: poly(ADP-ribose) glycohydrolase.
Gene Ontology
Molecular Function
GO:0004649 poly(ADP-ribose) glycohydrolase activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006282 regulation of DNA repair

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:4na0, PDBe:4na0, PDBj:4na0
PDBsum4na0
PubMed24465839
UniProtO88622|PARG_MOUSE Poly(ADP-ribose) glycohydrolase (Gene Name=Parg)

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