3U4I

CD38 structure-based inhibitor design using the N1-cyclic inosine 5'-diphosphate ribose template

Structural Biology Knowledgebase: 3U4I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3U4I

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 61300.55

Macromolecule Entities
Molecule Chains Length Organism Details
ADP-ribosyl cyclase 1 A, B 262 Homo sapiens EC#: 3.2.2.6 IUBMB
Fragment: extracellular domain, enzymatic domain
Mutation: Q49T, N100D, N164D, N209D, N219D
Gene Name(s): CD38 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CVR
Query on CVR

A Cyclic adenosine 5'-diphosphocarbocyclic ribose
C16 H23 N5 O12 P2
WXTUXMLWWNQYJT-BKYLUIDASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CVR N/A in BindingDB
N/A in BindingMoad
IC50: 129000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.179
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.22 α = 105.20
b = 54.00 β = 91.08
c = 66.55 γ = 94.68

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-10-08
  • Released Date: 2012-10-10
  • Deposition author(s): Liu, Q., Hao, Q., Lee, H.C., Graeff, R.

Revision History

  • 2013-07-24
    Type: Citation | Details: Citation update