Structure of PDB 8dmt Chain D Binding Site BS01

Receptor Information
>8dmt Chain D (length=488) Species: 7227 (Drosophila melanogaster) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SWPAVTGDSPHLTNFGRKLLKDCRQVQKPIGGYENLGNVIKLSAEFPLEF
GVNSVKVYRQSPSRLARINEEVASAYPLIHERTLGLYLQYLEHKCRWGNA
VEKPIYRNLSLCGFVQRLLVKRCASFFARNDKYLLVSGESGASGFEAVGT
REEKAPLVLANVLSYDDIKLSALLSVSSRTEFVNEGERTNCGHVDLNTKT
LERHGVIVGMIGARLSRRNLMEFQDIVIARQQNTRERGYGMALDEPATTR
DEDYRRLWREFYATRDLIHGQAVIDNQRFGPSKNKMDVFDNLVMKRRYAI
SFDMLLLEAEARAKRVKKLAYIHVVGFGLGVWKAAEQQERIFMETFEQRM
RTLGNRLNNVGLVHFSWFSITHCGGLSNGSLIEIPGHPKDGIRVLISKRN
PARKLSDPEHAGMLLVVSYAWDGNALPGNEFWMKMLQSTGDSSTACSTLV
AELHNPYINTKFCNGGNLHIASPEHGVLHIAEYAKRVI
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 chain8dmt Chain D Residue 501 [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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PDB8dmt Structure of ADP-ribose-bound Drosophila macrodomain CG2909
Resolution2.28 Å
Binding residue
(original residue number in PDB)
R198 G336 F337 G338 G340 V341 W342 W377 A430 W431 D432 N439 T449 G450 D451
Binding residue
(residue number reindexed from 1)
R188 G326 F327 G328 G330 V331 W332 W367 A420 W421 D422 N429 T439 G440 D441
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003875 ADP-ribosylarginine hydrolase activity

View graph for
Molecular Function
External links
PDB RCSB:8dmt, PDBe:8dmt, PDBj:8dmt
PDBsum8dmt
PubMed38503748
UniProtQ9W2W5

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