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 3UW5 | pdb_00003uw5

Crystal structure of the BIR domain of MLIAP bound to GDC0152


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 
    0.166 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3UW5

This is version 1.5 of the entry. See complete history. 

Literature

Discovery of a Potent Small-Molecule Antagonist of Inhibitor of Apoptosis (IAP) Proteins and Clinical Candidate for the Treatment of Cancer (GDC-0152).

Flygare, J.A., Beresini, M., Budha, N., Chan, H., Chan, I.T., Cheeti, S., Cohen, F., Deshayes, K., Doerner, K., Eckhardt, S.G., Elliott, L.O., Feng, B., Franklin, M.C., Reisner, S.F., Gazzard, L., Halladay, J., Hymowitz, S.G., La, H., Lorusso, P., Maurer, B., Murray, L., Plise, E., Quan, C., Stephan, J.P., Young, S.G., Tom, J., Tsui, V., Um, J., Varfolomeev, E., Vucic, D., Wagner, A.J., Wallweber, H.J., Wang, L., Ware, J., Wen, Z., Wong, H., Wong, J.M., Wong, M., Wong, S., Yu, R., Zobel, K., Fairbrother, W.J.

(2012) J Med Chem 55: 4101-4113

  • DOI: https://doi.org/10.1021/jm300060k
  • Primary Citation Related Structures: 
    3UW4, 3UW5

  • PubMed Abstract: 

    A series of compounds were designed and synthesized as antagonists of cIAP1/2, ML-IAP, and XIAP based on the N-terminus, AVPI, of mature Smac. Compound 1 (GDC-0152) has the best profile of these compounds; it binds to the XIAP BIR3 domain, the BIR domain of ML-IAP, and the BIR3 domains of cIAP1 and cIAP2 with K(i) values of 28, 14, 17, and 43 nM, respectively. These compounds promote degradation of cIAP1, induce activation of caspase-3/7, and lead to decreased viability of breast cancer cells without affecting normal mammary epithelial cells. Compound 1 inhibits tumor growth when dosed orally in the MDA-MB-231 breast cancer xenograft model. Compound 1 was advanced to human clinical trials, and it exhibited linear pharmacokinetics over the dose range (0.049 to 1.48 mg/kg) tested. Mean plasma clearance in humans was 9 ± 3 mL/min/kg, and the volume of distribution was 0.6 ± 0.2 L/kg.


  • Organizational Affiliation: 
    • Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA. jflygare@gene.com

Macromolecule Content 

  • Total Structure Weight: 27.47 kDa 
  • Atom Count: 1,748 
  • Modeled Residue Count: 190 
  • Deposited Residue Count: 240 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 7, Baculoviral IAP repeat-containing protein 4
A, B
116Homo sapiensMutation(s): 1 
Gene Names: BIRC7, KIAP, LIVIN, MLIAP, RNF50, UNQ5800/PRO19607/PRO21344, API3, BIRC4, IAP3, XIAP
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens)
Explore P98170 
Go to UniProtKB:  P98170
PHAROS:  P98170
GTEx:  ENSG00000101966 
Find proteins for Q96CA5 (Homo sapiens)
Explore Q96CA5 
Go to UniProtKB:  Q96CA5
PHAROS:  Q96CA5
GTEx:  ENSG00000101197 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP98170Q96CA5
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GDC-0152C [auth Z],
D [auth Y]
4N/AMutation(s): 0 
Sequence Annotations
Expand
Reference Sequence

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free:  0.166 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.396α = 90
b = 87.396β = 90
c = 73.466γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 1.2: 2012-05-23
    Changes: Database references
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.5: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary