Structure of PDB 3dzi Chain B Binding Site BS01

Receptor Information

>3dzi Chain B (length=252) Species: 9606 (Homo sapiens)

RWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFI
SKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFT
LEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSR
RFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIH
GGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDS
SC

Ligand information

• Ligand ID: N
• InChI: InChI=1S/C5H11O7P/c6-3-1-11-4(5(3)7)2-12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5-/m0/s1
• InChIKey: CYZZKTRFOOKUMT-LMVFSUKVSA-N
• SMILES:
  ACDLabs 10.04: O=P(OCC1OCC(O)C1O)(O)O
  CACTVS 3.385: O[CH]1CO[CH](CO[P](O)(O)=O)[CH]1O
  OpenEye OEToolkits 1.7.5: C1C(C(C(O1)COP(=O)(O)O)O)O
  CACTVS 3.385: O[C@H]1CO[C@H](CO[P](O)(O)=O)[C@H]1O
  OpenEye OEToolkits 1.7.5: C1[C@@H]([C@@H]([C@H](O1)COP(=O)(O)O)O)O
• Formula: C5 H11 O7 P
• Name: ANY 5'-MONOPHOSPHATE NUCLEOTIDE;
  1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE
• ZINC: ZINC000005850787
• PDB chain: 3dzi Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dzi Covalent and Noncovalent Intermediates of an NAD Utilizing Enzyme, Human CD38.
• Resolution: 1.73 Å
• Binding residue (original residue number in PDB): L124 W125 S126 R127 L145 S220 T221 F222 E226
• Binding residue (residue number reindexed from 1): L80 W81 S82 R83 L101 S176 T177 F178 E182
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): E146 T221 E226
• Catalytic site (residue number reindexed from 1): E102 T177 E182
• 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

External links

• PDB: RCSB:3dzi, PDBe:3dzi, PDBj:3dzi
• PDBsum: 3dzi
• PubMed: 18940667
• UniProt: P28907|CD38_HUMAN ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 (Gene Name=CD38)