3EYL

Crystal structure of XIAP BIR3 domain in complex with a Smac-mimetic compound

Structural Biology Knowledgebase: 3EYL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EYL

Classification: LIGASE

Total Structure Weight: 29387.68

Macromolecule Entities
Molecule Chains Length Organism Details
Baculoviral IAP repeat-containing protein 4 A, B 122 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
SMK
Query on SMK

A, B (3S,6S,7R,9aS)-6-{[(2S)-2-aminobutanoyl]amino}- 7-(2-aminoethyl)-N-(diphenylmethyl)-5-oxooctahydro- 1H-pyrrolo[1,2-a]azepine-3-carboxamide
C29 H39 N5 O3
KQHWCFZCUNTTCW-VEGWMBEDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SMK IC50: 86 - 250 nM (100) BindingDB
Ki: 220 nM (100) BindingDB

N/A in BindingMoad
IC50: 250 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.189
  • Space Group: I 41 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 170.42 α = 90.00
b = 170.42 β = 90.00
c = 170.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-10-21
  • Released Date: 2008-11-25
  • Deposition author(s): Cossu, F., Milani, M., Mastrangelo, E., Bolognesi, M.

Revision History

  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor