3F7G | pdb_00003f7g

Structure of the BIR domain from ML-IAP bound to a peptidomimetic

PDB DOI: https://doi.org/10.2210/pdb3F7G/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.209 (Depositor), 0.212 (DCC)
R-Value Work:
0.167 (Depositor), 0.173 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/jm801450c
Primary Citation 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.

Organizational Affiliation

Departments of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA. fcohen@gene.com

Macromolecule Content

Total Structure Weight: 79.94 kDa
Atom Count: 4,283
Modeled Residue Count: 495
Deposited Residue Count: 700
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baculoviral IAP repeat-containing protein 7	A, B, C, D, E	140	Homo sapiens	Mutation(s): 0 Gene Names: also known as KIAP OR MLIAP OR LIVIN, 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 GTEx: ENSG00000101197
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96CA5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
389 Query on 389 Download:Ideal Coordinates CCD File SDF format, chain K [auth E] MOL2 format, chain K [auth E] mmCIF format, chain K [auth E]	K [auth E]	L-alanyl-L-valyl-N-(2,2-diphenylethyl)-L-prolinamide C₂₇ H₃₆ N₄ O₃ ZJCCVSICICQPSQ-IGKWTDBASA-N		Interactions Focus chain K [auth E] Interactions & Density Focus chain K [auth E]
P33 Query on P33 Download:Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth E] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth E] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B], H [auth C], I [auth D], L [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain L [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain L [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
389	BindingDB: 3F7G	Ki: 43 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.209 (Depositor), 0.212 (DCC)
R-Value Work: 0.167 (Depositor), 0.173 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.016	α = 90
b = 84.016	β = 90
c = 94.476	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Franklin, M.C.

Fairbrother, W.J.

Cohen, F.

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary