3UW5

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 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 10.1021/jm300060k
  • Primary Citation of Related Structures:  
    3UW5, 3UW4

  • 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 7, Baculoviral IAP repeat-containing protein 4A, B116Homo sapiensMutation(s): 1 
Gene Names: BIRC7KIAPLIVINMLIAPRNF50UNQ5800/PRO19607/PRO21344API3BIRC4IAP3XIAP
EC: 2.3.2.27
Find proteins for P98170 (Homo sapiens)
Explore P98170 
Go to UniProtKB:  P98170
NIH Common Fund Data Resources
PHAROS:  P98170
Find proteins for Q96CA5 (Homo sapiens)
Explore Q96CA5 
Go to UniProtKB:  Q96CA5
NIH Common Fund Data Resources
PHAROS:  Q96CA5
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GDC-0152D [auth Y], C [auth Z]4N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], H [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], G [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MAA
Query on MAA
C [auth Z], D [auth Y]L-PEPTIDE LINKINGC4 H9 N O2ALA
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001020
Query on PRD_001020
C [auth Y], D [auth Z]GDC0152Peptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • 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