4TUH

Bcl-xL in complex with inhibitor (Compound 10)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Guided Rescaffolding of Selective Antagonists of BCL-XL.

Koehler, M.F.Bergeron, P.Choo, E.F.Lau, K.Ndubaku, C.Dudley, D.Gibbons, P.Sleebs, B.E.Rye, C.S.Nikolakopoulos, G.Bui, C.Kulasegaram, S.Kersten, W.J.Smith, B.J.Czabotar, P.E.Colman, P.M.Huang, D.C.Baell, J.B.Watson, K.G.Hasvold, L.Tao, Z.F.Wang, L.Souers, A.J.Elmore, S.W.Flygare, J.A.Fairbrother, W.J.Lessene, G.

(2014) ACS Med Chem Lett 5: 662-667

  • DOI: https://doi.org/10.1021/ml500030p
  • Primary Citation of Related Structures:  
    4TUH

  • PubMed Abstract: 

    Because of the promise of BCL-2 antagonists in combating chronic lymphocytic leukemia (CLL) and non-Hodgkin's lymphoma (NHL), interest in additional selective antagonists of antiapoptotic proteins has grown. Beginning with a series of selective, potent BCL-XL antagonists containing an undesirable hydrazone functionality, in silico design and X-ray crystallography were utilized to develop alternative scaffolds that retained the selectivity and potency of the starting compounds.


  • Organizational Affiliation

    Departments of Discovery Chemistry, Drug Metabolism and Pharmacokinetics, and Early Discovery Biochemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bcl-2-like protein 1
A, B, C, D, E
A, B, C, D, E, F, G, H
158Homo sapiensMutation(s): 0 
Gene Names: BCL2L1BCL2LBCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
GTEx:  ENSG00000171552 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07817
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
38H
Query on 38H

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
I [auth A]
Q [auth B]
S [auth C]
AA [auth G],
CA [auth H],
I [auth A],
Q [auth B],
S [auth C],
W [auth D],
X [auth E],
Y [auth F]
2-[8-(1,3-benzothiazol-2-ylcarbamoyl)-3,4-dihydroisoquinolin-2(1H)-yl]-5-{3-[4-(1H-pyrazolo[3,4-d]pyrimidin-1-yl)phenoxy]propyl}-1,3-thiazole-4-carboxylic acid
C35 H28 N8 O4 S2
LMOJCFKMCAPGGY-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
EA [auth H]
J [auth A]
K [auth A]
BA [auth G],
DA [auth H],
EA [auth H],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
T [auth C],
U [auth C],
V [auth C],
Z [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
R [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.834α = 90
b = 109.661β = 91.77
c = 102.099γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Data collection, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Refinement description