3CM7

Crystal Structure of XIAP-BIR3 domain in complex with Smac-mimetic compuond, Smac005

Structural Biology Knowledgebase: 3CM7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.300
  • R-Value Work: 0.233

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3CM7

Classification: Ligase Apoptosis

Total Structure Weight: 61919.00

Macromolecule Entities
Molecule Chains Length Organism Details
Baculoviral IAP repeat-containing protein 4 A, B, C, D 130 Homo sapiens EC#: 6.3.2 IUBMB
Fragment: UNP residues 241-356
Gene Name(s): XIAP Gene View API3 BIRC4 IAP3

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
X22
Query on X22

A, B, C, D (3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}- N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro- 1H-pyrrolo[1,2-a]azepine-3-carboxamide
2(S),3(S),6(S),7(S),9a(S) 6-(2-Amino-butyrylamino)- 7-hydroxymethyl-5-oxo-octahydro-pyrrolo[1,2- a]azepine-3-carboxylic acid benzhydryl-amide (Synonym)
C28 H36 N4 O4
WXYVFFGXHFXTLU-FCRIMTMASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
X22 IC50: 270 - 290 nM (98 - 100) BindingDB
Ki: 250 nM (100) BindingDB

N/A in BindingMoad
IC50: 270 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.300
  • R-Value Work: 0.233
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 92.39 α = 90.00
b = 92.39 β = 90.00
c = 175.15 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-03-21
  • Released Date: 2008-10-28
  • Deposition author(s): Mastrangelo, E., Cossu, F., Milani, M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4