Structure of PDB 2pgl Chain A Binding Site BS01

Receptor Information
>2pgl Chain A (length=252) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFI
SKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFT
LEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSR
RFAEAACDVVHVMLDGSRSKIFDKDSTFGSVQVHNLQPEKVQTLEAWVIH
GGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDS
SC
Ligand information
Ligand IDN1C
InChIInChI=1S/C15H20N4O14P2/c20-8-5-1-29-34(25,26)33-35(27,28)30-2-6-9(21)11(23)15(32-6)19-4-17-12-7(13(19)24)16-3-18(12)14(31-5)10(8)22/h3-6,8-11,14-15,20-23H,1-2H2,(H,25,26)(H,27,28)/t5?,6-,8-,9-,10-,11-,14-,15-/m1/s1
InChIKeyREBZYOYBILSKBL-ATYUDWGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.352O[CH]1[CH](O)[CH]2O[CH]1CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5C(=O)[N]2C=Nc45
OpenEye OEToolkits 1.7.0c1nc2c3n1C4C(C(C(O4)COP(=O)(OP(=O)(OCC5C(C(C(O5)N(C2=O)C=N3)O)O)O)O)O)O
ACDLabs 11.02O=C2N3C=Nc1n(cnc12)C5OC(COP(=O)(O)OP(=O)(O)OCC4OC3C(O)C4O)C(O)C5O
OpenEye OEToolkits 1.7.0c1nc2c3n1[C@H]4[C@@H](C(C(O4)CO[P@@](=O)(O[P@](=O)(OC[C@@H]5[C@H]([C@H]([C@@H](O5)N(C2=O)C=N3)O)O)O)O)O)O
CACTVS 3.352O[C@H]1[C@@H](O)[C@H]2O[C@@H]1CO[P](O)(=O)O[P](O)(=O)OC[C@@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5C(=O)[N@]2C=Nc45
FormulaC15 H20 N4 O14 P2
NameN1-CYCLIC INOSINE 5'-DIPHOSPHORIBOSE
ChEMBL
DrugBank
ZINC
PDB chain2pgl Chain A Residue 301 [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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PDB2pgl Catalysis-associated Conformational Changes Revealed by Human CD38 Complexed with a Non-hydrolyzable Substrate Analog
Resolution1.76 Å
Binding residue
(original residue number in PDB)		L124 W125 S126 R127 L145 E146 W189 S193 T221 F222 Q226
Binding residue
(residue number reindexed from 1)		L80 W81 S82 R83 L101 E102 W145 S149 T177 F178 Q182
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.59,IC50=0.26mM
Enzymatic activity
Catalytic site (original residue number in PDB) E146 T221 Q226
Catalytic site (residue number reindexed from 1) E102 T177 Q182
Enzyme Commision number 2.4.99.20: 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase.
3.2.2.-
3.2.2.6: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase.
Gene Ontology
Molecular Function
GO:0061809 NAD+ nucleotidase, cyclic ADP-ribose generating

View graph for
Molecular Function
External links
PDB RCSB:2pgl, PDBe:2pgl, PDBj:2pgl
PDBsum2pgl
PubMed17591784
UniProtP28907|CD38_HUMAN ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 (Gene Name=CD38)

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