Structure of PDB 4b1j Chain A Binding Site BS01

Receptor Information
>4b1j Chain A (length=508) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPT
HYKDLWDNKHVKMPCSEQNLYPVERTAGSRWELIQTALLNKFTRPQNLKD
AILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLP
NICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSS
YPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTAAAPTGLVTFTRQSLEDF
PEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQE
EIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSH
EDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRP
GVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDS
ELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPF
IYHAVESC
Ligand information
Ligand IDA1R
InChIInChI=1S/C15H24N6O12P2/c16-13-9-14(19-4-18-13)21(5-20-9)15-12(25)11(24)8(32-15)3-31-35(28,29)33-34(26,27)30-2-6-10(23)7(22)1-17-6/h4-8,10-12,15,17,22-25H,1-3H2,(H,26,27)(H,28,29)(H2,16,18,19)/t6-,7+,8-,10-,11-,12-,15-/m1/s1
InChIKeyNDQDTBCXPOIQGT-UHNJQBFTSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(OCC1NCC(O)C1O)OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H](CN4)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(CN4)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4NC[CH](O)[CH]4O)[CH](O)[CH]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]4NC[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
FormulaC15 H24 N6 O12 P2
Name5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
ChEMBLCHEMBL1230692
DrugBank
ZINCZINC000016052290
PDB chain4b1j Chain A Residue 1966 [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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PDB4b1j Structures of the Human Poly (Adp-Ribose) Glycohydrolase Catalytic Domain Confirm Catalytic Mechanism and Explain Inhibition by Adp-Hpd Derivatives.
Resolution2.08 Å
Binding residue
(original residue number in PDB)		I726 E727 F738 N740 V753 Q754 E755 E756 Y795 N869 G871 G873 A874 F875 F902
Binding residue
(residue number reindexed from 1)		I271 E272 F283 N285 V298 Q299 E300 E301 Y340 N414 G416 G418 A419 F420 F447
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=7.30,Kd=50.0nM
BindingDB: IC50=120nM
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:4b1j, PDBe:4b1j, PDBj:4b1j
PDBsum4b1j
PubMed23251397
UniProtQ86W56|PARG_HUMAN Poly(ADP-ribose) glycohydrolase (Gene Name=PARG)

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