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 

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:  

  • 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 do ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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), XIAP (API3, BIRC4, IAP3)
EC: 2.3.2.27 2.3.2.27
Find proteins for Q96CA5 (Homo sapiens)
Go to Gene View: BIRC7
Go to UniProtKB:  Q96CA5
Find proteins for P98170 (Homo sapiens)
Go to Gene View: XIAP
Go to UniProtKB:  P98170
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GDC-0152
Z, Y
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001020
Query on PRD_001020
Y,ZGDC0152Peptide-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 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.396α = 90.00
b = 87.396β = 90.00
c = 73.466γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
Blu-Icedata collection
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references
  • Version 1.2: 2012-05-23
    Type: Database references
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2017-08-02
    Type: Refinement description, Source and taxonomy