3CM2

Crystal Structure of XIAP BIR3 domain in complex with a Smac-mimetic compound, Smac010

Structural Biology Knowledgebase: 3CM2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.221

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3CM2

Classification: Ligase Apoptosis

Total Structure Weight: 152324.12

Macromolecule Entities
Molecule Chains Length Organism Details
Baculoviral IAP repeat-containing protein 4 A, B, C..., D, E, F, G, H, I, JA, B, C, D, E, F, G, H, I, J 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
X23
Query on X23

A, B, C, D, E, F, G, H, I, J (3S,6S,7R,9aS)-6-{[(2S)-2-aminobutanoyl]amino}- 7-(aminomethyl)-N-(diphenylmethyl)-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-aminomethyl-5-oxo-octahydro-pyrrolo[1,2- a]azepine-3-carboxylic acid benzhydryl-amide (Synonym)
C28 H37 N5 O3
XXJHZERDDCOFPK-FCRIMTMASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D, E, F, G, H, I, J ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
X23 IC50: 110 - 970 nM (98 - 100) BindingDB
Ki: 870 nM (100) BindingDB

IC50: 970 nM  BindingMOAD
Ki: 340 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.221
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 77.53 α = 90.00
b = 108.35 β = 90.00
c = 225.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-03-20
  • Released Date: 2008-10-28
  • Deposition author(s): Cossu, F., Mastrangelo, E., Milani, M.

Revision History

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