3F7H

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

• PDB DOI:  https://doi.org/10.2210/pdb3F7H/pdb

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


• Deposited: 2008-11-09 Released: 2009-03-17 
• Deposition Author(s): Franklin, M.C., Fairbrother, W.J., Cohen, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.175 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Literature

Orally bioavailable antagonists of inhibitor of apoptosis proteins based on an azabicyclooctane scaffold

Cohen, F., Alicke, B., Elliott, L.O., Flygare, J.A., Goncharov, T., Keteltas, S.F., Franklin, M.C., Frankovitz, S., Stephan, J.P., Tsui, V., Vucic, D., Wong, H., Fairbrother, W.J.

(2009) J Med Chem 52: 1723-1730

• PubMed: 19228017 
• DOI: https://doi.org/10.1021/jm801450c
• Primary Citation of Related Structures:  
  3F7G, 3F7H, 3F7I


• PubMed Abstract: 
  

A series of IAP antagonists based on an azabicyclooctane scaffold was designed and synthesized. The most potent of these compounds, 14b, binds to the XIAP BIR3 domain, the BIR domain of ML-IAP, and the BIR3 domain of c-IAP1 with K(i) values of 140, 38, and 33 nM, respectively. These compounds promote degradation of c-IAP1, activate caspases, and lead to decreased viability of breast cancer cells without affecting normal mammary epithelial cells. Finally, compound 14b inhibits tumor growth when dosed orally in a breast cancer xenograft model.

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Related Citations: 

• Design, synthesis, and biological activity of a potent Smac mimetic that sensitizes cancer cells to apoptosis by antagonizing IAPs.
  Zobel, K., Wang, L., Varfolomeev, E., Franklin, M.C., Elliott, L.O., Wallweber, H.J., Okawa, D.C., Flygare, J.A., Vucic, D., Fairbrother, W.J., Deshayes, K.
  (2006) ACS Chem Biol 1: 525

• Engineering ML-IAP to produce an extraordinarily potent caspase-9 inhibitor: implications for Smac-dependent anti-apoptotic activity of ML-IAP.
  Vucic, D., Franklin, M.C., Wallweber, H.J., Das, K., Eckelman, B.P., Shin, H., Elliott, L.O., Deshayes, K., Salvesen, G.S., Fairbrother, W.J.
  (2005) Biochem J 385: 11

• Structure and function analysis of peptide antagonists of melanoma inhibitor of apoptosis (ML-IAP)
  Franklin, M.C., Kadkhodayan, S., Ackerly, H., Alexandru, D., Distefano, M.D., Elliott, L.O., Flygare, J.A., Vucic, D., Deshayes, K., Fairbrother, W.J.
  (2003) Biochemistry 42: 8223

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Organizational Affiliation: 

Departments of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 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: 31.46 kDa 
• Atom Count: 1,789 
• Modelled Residue Count: 183 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baculoviral IAP repeat-containing protein 7	A, B	133	Homo sapiens	Mutation(s): 11  Gene Names: BIRC7, KIAP, LIVIN, MLIAP, RNF50, UNQ5800/PRO19607/PRO21344 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
419	D [auth A], G [auth B]	N-[(3aR,6S,6aS)-1-(N-methyl-L-alanyl-3-methyl-L-valyl)octahydrocyclopenta[b]pyrrol-6-yl]-2,2-diphenylacetamide C31 H42 N4 O3 BGWQMUKSEXDJIL-PCVPZPMISA-N
BTB	H [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
LI	F [auth B]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
419	BindingDB:  3F7H	Ki: 82 (nM) from 1 assay(s)
	PDBBind:  3F7H	Ki: 82 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.175 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.048	α = 90
b = 88.048	β = 90
c = 73.321	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Franklin, M.C., Fairbrother, W.J., Cohen, F.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations