4WVS

Crystal structure of XIAP-BIR2 domain complexed with (S)-3-(4-methoxyphenyl)-2-((S)-2-((S)-1-((S)-2-((S)-2-(methylamino)propanamido)pent-4-ynoyl)pyrrolidine-2-carboxamido)-3-phenylpropanamido)propanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.164 

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:  

  • 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 suggeste ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase XIAP
A
98Homo sapiensMutation(s): 2 
Gene Names: XIAP (API3, BIRC4, IAP3)
EC: 2.3.2.27
Find proteins for P98170 (Homo sapiens)
Go to Gene View: XIAP
Go to UniProtKB:  P98170
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
3,11-DIFLUORO-6,8,13-TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN-13-IUM
B
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
LPH
Query on LPH
B
L-peptide linkingC5 H7 N O2

--

4LZ
Query on 4LZ
B
L-PEPTIDE LINKINGC11 H15 N4 O3TYR
MAA
Query on MAA
B
L-peptide linkingC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 28.187α = 90.00
b = 39.269β = 94.53
c = 32.947γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-11-07 
  • Released Date: 2015-05-06 
  • Deposition Author(s): Pokross, M.E.

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Derived calculations, Refinement description, Source and taxonomy