Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.01 kDa 
• Atom Count: 1004 
• Modelled Residue Count: 106 
• Deposited Residue Count: 110 
• Unique protein chains: 1

5C7A

Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Compound 7

• PDB DOI: 10.2210/pdb5C7A/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-24 Released: 2015-08-12 
• Deposition Author(s): Chessari, G., Buck, I.M., Day, J.E.H., Day, P.J., Iqbal, A., Johnson, C.N., Lewis, E.J., Martins, V., Miller, D., Reader, M., Rees, D.C., Rich, S.J., Tamanini, E., Vitorino, M., Ward, G.A., Williams, P.A., Williams, G., Wilsher, N.E., Woolford, A.J.-A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.264 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Discovery of a Non-Alanine Lead Series with Dual Activity Against cIAP1 and XIAP.

Chessari, G., Buck, I.M., Day, J.E., Day, P.J., Iqbal, A., Johnson, C.N., Lewis, E.J., Martins, V., Miller, D., Reader, M., Rees, D.C., Rich, S.J., Tamanini, E., Vitorino, M., Ward, G.A., Williams, P.A., Williams, G., Wilsher, N.E., Woolford, A.J.

(2015) J Med Chem 58: 6574-6588

• PubMed: 26218264 
• DOI: 10.1021/acs.jmedchem.5b00706
• Primary Citation of Related Structures:  
  5C0K, 5C0L, 5C3H, 5C3K, 5C7A, 5C7B, 5C7C, 5C7D, 5C83, 5C84


• PubMed Abstract: 
  

Inhibitor of apoptosis proteins (IAPs) are important regulators of apoptosis and pro-survival signaling pathways whose deregulation is often associated with tumor genesis and tumor growth. IAPs have been proposed as targets for anticancer therapy, and a number of peptidomimetic IAP antagonists have entered clinical trials. Using our fragment-based screening approach, we identified nonpeptidic fragments binding with millimolar affinities to both cellular inhibitor of apoptosis protein 1 (cIAP1) and X-linked inhibitor of apoptosis protein (XIAP). Structure-based hit optimization together with an analysis of protein-ligand electrostatic potential complementarity allowed us to significantly increase binding affinity of the starting hits. Subsequent optimization gave a potent nonalanine IAP antagonist structurally distinct from all IAP antagonists previously reported. The lead compound had activity in cell-based assays and in a mouse xenograft efficacy model and represents a highly promising start point for further optimization.

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Organizational Affiliation: 

Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase XIAP	A	110	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4YE	C [auth A]	(2R)-4-[2-(2,3-dihydro-1H-indol-1-yl)-2-oxoethyl]-2-methylpiperazin-1-ium C15 H22 N3 O ZKEAJFPUDNSYIF-GFCCVEGCSA-O
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.264 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.401	α = 90
b = 71.401	β = 90
c = 105.242	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-06-24 
• Released Date: 2015-08-12 
Deposition Author(s): Chessari, G., Buck, I.M., Day, J.E.H., Day, P.J., Iqbal, A., Johnson, C.N., Lewis, E.J., Martins, V., Miller, D., Reader, M., Rees, D.C., Rich, S.J., Tamanini, E., Vitorino, M., Ward, G.A., Williams, P.A., Williams, G., Wilsher, N.E., Woolford, A.J.-A.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Database references