5M6M | pdb_00005m6m

Small Molecule inhibitors of IAP

• PDB DOI: https://doi.org/10.2210/pdb5M6M/pdb

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


• Deposited: 2016-10-25 Released: 2017-05-24 
• Deposition Author(s): Williams, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Discovery of a Potent Nonpeptidomimetic, Small-Molecule Antagonist of Cellular Inhibitor of Apoptosis Protein 1 (cIAP1) and X-Linked Inhibitor of Apoptosis Protein (XIAP).

Tamanini, E., Buck, I.M., Chessari, G., Chiarparin, E., Day, J.E.H., Frederickson, M., Griffiths-Jones, C.M., Hearn, K., Heightman, T.D., Iqbal, A., Johnson, C.N., Lewis, E.J., Martins, V., Peakman, T., Reader, M., Rich, S.J., Ward, G.A., Williams, P.A., Wilsher, N.E.

(2017) J Med Chem 60: 4611-4625

• PubMed: 28492317 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b01877
• Primary Citation of Related Structures:  
  5M6E, 5M6F, 5M6H, 5M6L, 5M6M, 5M6N


• PubMed Abstract: 
  

  XIAP and cIAP1 are members of the inhibitor of apoptosis protein (IAP) family and are key regulators of anti-apoptotic and pro-survival signaling pathways. Overexpression of IAPs occurs in various cancers and has been associated with tumor progression and resistance to treatment. Structure-based drug design (SBDD) guided by structural information from X-ray crystallography, computational studies, and NMR solution conformational analysis was successfully applied to a fragment-derived lead resulting in AT-IAP, a potent, orally bioavailable, dual antagonist of XIAP and cIAP1 and a structurally novel chemical probe for IAP biology.

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Organizational Affiliation: 

Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 15.14 kDa 
• Atom Count: 1,093 
• Modelled Residue Count: 104 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase XIAP	A	127	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 GTEx:  ENSG00000101966

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7H8	D [auth A]	1-[[(2~{R},5~{R})-1-[2-[3,3-dimethyl-6-(phenylmethyl)-2~{H}-pyrrolo[3,2-b]pyridin-1-yl]-2-oxidanylidene-ethyl]-5-methyl-piperazin-4-ium-2-yl]methyl]pyrrolidin-2-one C28 H38 N5 O2 ALAFRPAHGDJVFE-NFBKMPQASA-O
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.134	α = 90
b = 71.134	β = 90
c = 105.614	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Williams, P.A.

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2017-06-21
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations