4WVU

CRYSTAL STRUCTURE OF XIAP-BIR2 DOMAIN COMPLEXED WITH LIGAND BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1021/jm501892g
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase XIAPA98Homo sapiensMutation(s): 2 
Gene Names: XIAPAPI3BIRC4IAP3
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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
3,11-DIFLUORO-6,8,13-TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN-13-IUMB5N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
HOX
Query on HOX
BL-PEPTIDE LINKINGC9 H12 N2 O2PHE
MAA
Query on MAA
BL-PEPTIDE LINKINGC4 H9 N O2ALA
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.261α = 90
b = 39.328β = 95.51
c = 33.058γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2014-11-07 
  • Released Date: 2015-03-04 
  • Deposition Author(s): Pokross, M.E.

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