4TUH | pdb_00004tuh

Bcl-xL in complex with inhibitor (Compound 10)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 38HClick on this verticalbar to view details

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
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]
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]
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
Binding Affinity Annotations 
IDSourceBinding Affinity
38H BindingDB:  4TUH Ki: min: 0.04, max: 0.38 (nM) from 2 assay(s)
EC50: 60 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 38HClick on this verticalbar to view details

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