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 3UW4 | pdb_00003uw4

Crystal structure of cIAP1 BIR3 bound to GDC0152


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.221 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3UW4

This is version 1.6 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: 11.25 kDa 
  • Atom Count: 801 
  • Modeled Residue Count: 91 
  • Deposited Residue Count: 96 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 2, Baculoviral IAP repeat-containing protein 492Homo sapiensMutation(s): 3 
Gene Names: API1, BIRC2, cIAP1, IAP2, MIHB, RNF48, 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 Q13490 (Homo sapiens)
Explore Q13490 
Go to UniProtKB:  Q13490
PHAROS:  Q13490
GTEx:  ENSG00000110330 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP98170Q13490
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GDC0152B [auth Z]4N/AMutation(s): 0 
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CHG
Query on CHG
B [auth Z]L-PEPTIDE LINKINGC8 H15 N O2

--

MAA
Query on MAA
B [auth Z]L-PEPTIDE LINKINGC4 H9 N O2ALA

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.221 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.691α = 90
b = 37.38β = 90
c = 57.598γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2023-12-06
    Changes: Data collection