Structure of PDB 2l8r Chain A Binding Site BS01

Receptor Information
>2l8r Chain A (length=150) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSLNEDPEGSRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKF
GGVQELLNQQKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLEA
MKSHCLKNGVTDLSMPRIGCGLDRLQWENVSAMIEEVFEATDIKITVYTL
Ligand information
Ligand IDAPR
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-KEOHHSTQSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)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]([C@@H](O4)O)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(C(O4)O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(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
CACTVS 3.341Nc1ncnc2n(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
FormulaC15 H23 N5 O14 P2
NameADENOSINE-5-DIPHOSPHORIBOSE
ChEMBLCHEMBL1231026
DrugBank
ZINCZINC000017654550
PDB chain2l8r Chain A Residue 186 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2l8r Orphan Macrodomain Protein (Human C6orf130) Is an O-Acyl-ADP-ribose Deacylase: SOLUTION STRUCTURE AND CATALYTIC PROPERTIES.
ResolutionN/A
Binding residue
(original residue number in PDB)		D20 L21 F22 C33 I34 I44 P118 R119 I120 D125 Y150 L152
Binding residue
(residue number reindexed from 1)		D18 L19 F20 C31 I32 I42 P116 R117 I118 D123 Y148 L150
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=3.92,Ki=119.3uM
Enzymatic activity
Enzyme Commision number 3.2.2.-
3.5.1.-
Gene Ontology
Molecular Function
GO:0001883 purine nucleoside binding
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0061463 O-acetyl-ADP-ribose deacetylase activity
GO:0140293 ADP-ribosylglutamate hydrolase activity
Biological Process
GO:0006974 DNA damage response
GO:0042278 purine nucleoside metabolic process
GO:0051725 protein de-ADP-ribosylation
GO:0140291 peptidyl-glutamate ADP-deribosylation
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005730 nucleolus
GO:0090734 site of DNA damage

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2l8r, PDBe:2l8r, PDBj:2l8r
PDBsum2l8r
PubMed21849506
UniProtQ9Y530|OARD1_HUMAN ADP-ribose glycohydrolase OARD1 (Gene Name=OARD1)

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