Structure of PDB 6edr Chain A Binding Site BS01

Receptor Information
>6edr Chain A (length=249) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRWRQQWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAF
ISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMF
TLEDTLLGYLADDLTWCGEFATSKINYQSCPDWRKDCSNNPVSVFWKTVS
RRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVI
HGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPE
Ligand information
Ligand IDZNA
InChIInChI=1S/C21H27N7O13P2S/c22-17-12-19(25-7-24-17)28(8-26-12)20-15(31)13(29)10(40-20)5-38-42(34,35)41-43(36,37)39-6-11-14(30)16(32)21(44-11)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/p+1/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyYLEHCOOOOOOSDX-NNYOXOHSSA-O
SMILES
SoftwareSMILES
CACTVS 3.385NC(=O)c1ccc[n+](c1)[CH]2S[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 2.0.7c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](S2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
ACDLabs 12.01Nc1ncnc2c1ncn2C1OC(COP(=O)(O)OP(=O)(O)OCC2SC([n+]3cc(ccc3)C(N)=O)C(O)C2O)C(O)C1O
CACTVS 3.385NC(=O)c1ccc[n+](c1)[C@@H]2S[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 2.0.7c1cc(c[n+](c1)C2C(C(C(S2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O13 P2 S
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain6edr Chain A Residue 401 [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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PDB6edr Facile chemoenzymatic synthesis of a novel stable mimic of NAD.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
W125 S126 R127 E146 W189 T221 F222
Binding residue
(residue number reindexed from 1)
W82 S83 R84 E103 W146 T178 F179
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=4.55,Ki=28.5uM
Enzymatic activity
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:6edr, PDBe:6edr, PDBj:6edr
PDBsum6edr
PubMed30568770
UniProtP28907|CD38_HUMAN ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 (Gene Name=CD38)

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