3U4H

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

Structural Biology Knowledgebase: 3U4H SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3U4H

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 61875.83

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
C8R
Query on C8R

A, B 8-Amino-N1-Cyclic Inosine 5'-Diphosphoribose
C15 H21 N5 O14 P2
RNYBVHDVCKIICB-AIKIOGRUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
C8R N/A in BindingDB
N/A in BindingMoad
IC50: 56000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.186
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 41.71 α = 72.85
b = 51.46 β = 89.13
c = 67.75 γ = 83.18

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