4WVT | pdb_00004wvt

Crystal structure of XIAP-BIR2 domain complexed with ligand bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.230 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4WVT

This is version 1.2 of the entry. See complete history. 

Literature

The Discovery of Macrocyclic XIAP Antagonists from a DNA-Programmed Chemistry Library, and Their Optimization To Give Lead Compounds with in Vivo Antitumor Activity.

Seigal, B.A., Connors, W.H., Fraley, A., Borzilleri, R.M., Carter, P.H., Emanuel, S.L., Fargnoli, J., Kim, K., Lei, M., Naglich, J.G., Pokross, M.E., Posy, S.L., Shen, H., Surti, N., Talbott, R., Zhang, Y., Terrett, N.K.

(2015) J Med Chem 58: 2855-2861

  • DOI: https://doi.org/10.1021/jm501892g
  • Primary Citation Related Structures: 
    4WVS, 4WVT, 4WVU

  • PubMed Abstract: 

    Affinity selection screening of macrocycle libraries derived from DNA-programmed chemistry identified XIAP BIR2 and BIR3 domain inhibitors that displace bound pro-apoptotic caspases. X-ray cocrystal structures of key compounds with XIAP BIR2 suggested potency-enhancing structural modifications. Optimization of dimeric macrocycles with similar affinity for both domains were potent pro-apoptotic agents in cancer cell lines and efficacious in shrinking tumors in a mouse xenograft model.

    • Organizational Affiliation: 
    • †Ensemble Therapeutics Corp, 99 Erie Street, Cambridge, Massachusetts 02139, United States.

Macromolecule Content 

  • Total Structure Weight: 24.41 kDa 
  • Atom Count: 1,571 
  • Modeled Residue Count: 170 
  • Deposited Residue Count: 208 
  • Unique protein chains: 2

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase XIAP
A, B
98Homo sapiensMutation(s): 2 
Gene Names: XIAP, API3, BIRC4, IAP3
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens)
Explore P98170 
Go to UniProtKB:  P98170
PHAROS:  P98170
GTEx:  ENSG00000101966 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98170
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
3,11-DIFLUORO-6,8,13-TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN-13-IUM
C, D
6N/AMutation(s): 0 

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MAA
Query on MAA
C, D
L-PEPTIDE LINKINGC4 H9 N O2ALA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.230 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.2α = 90
b = 38.53β = 89.83
c = 56.77γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
BUSTERrefinement
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references
  • Version 1.2: 2025-04-02
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary