3GT9

Structure of an ML-IAP/XIAP chimera bound to a peptidomimetic

• PDB DOI: https://doi.org/10.2210/pdb3GT9/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-03-27 Released: 2010-03-09 
• Deposition Author(s): Franklin, M.C., Fairbrother, W.J., Cohen, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.193 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Antagonists of inhibitor of apoptosis proteins based on thiazole amide isosteres.

Cohen, F., Koehler, M.F., Bergeron, P., Elliott, L.O., Flygare, J.A., Franklin, M.C., Gazzard, L., Keteltas, S.F., Lau, K., Ly, C.Q., Tsui, V., Fairbrother, W.J.

(2010) Bioorg Med Chem Lett 20: 2229-2233

• PubMed: 20189383 
• DOI: https://doi.org/10.1016/j.bmcl.2010.02.021
• Primary Citation of Related Structures:  
  3GT9, 3GTA


• PubMed Abstract: 
  

  A series of IAP antagonists based on thiazole or benzothiazole amide isosteres was designed and synthesized. These compounds were tested for binding to the XIAP-BIR3 and ML-IAP BIR using a fluorescence polarization assay. The most potent of these compounds, 19a and 33b, were found to have K(i)'s of 20-30 nM against ML-IAP and 50-60 nM against XIAP-BIR3.

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Organizational Affiliation: 

Department of Discovery Chemistry, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.1 kDa 
• Atom Count: 1,829 
• Modelled Residue Count: 179 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baculoviral IAP repeat-containing 7	A, B	133	Homo sapiens	Mutation(s): 11  Gene Names: BIRC7 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96CA5 (Homo sapiens) Explore Q96CA5  Go to UniProtKB:  Q96CA5
PHAROS:  Q96CA5 GTEx:  ENSG00000101197

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
516	D [auth A], F [auth B]	N-{(1S)-1-cyclohexyl-2-[(2S)-2-(4-naphthalen-1-yl-1,3-thiazol-2-yl)pyrrolidin-1-yl]-2-oxoethyl}-N~2~-methyl-L-alaninamide C29 H36 N4 O2 S OWHXKYSKEROHGU-CNVLFFCLSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
516	BindingDB:  3GT9	Ki: 1.10e+5 (nM) from 1 assay(s)
	PDBBind:  3GT9	Ki: 1.10e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.193 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.531	α = 90
b = 87.531	β = 90
c = 73.464	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Franklin, M.C., Fairbrother, W.J., Cohen, F.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-21
  Changes: Data collection
• Version 1.5: 2024-04-03
  Changes: Refinement description