7OKJ

Crystal structure of human BCL6 BTB domain in complex with compound 12c and its enantiomer 12b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Into Deep Water: Optimizing BCL6 Inhibitors by Growing into a Solvated Pocket.

Lloyd, M.G.Huckvale, R.Cheung, K.J.Rodrigues, M.J.Collie, G.W.Pierrat, O.A.Gatti Iou, M.Carter, M.Davis, O.A.McAndrew, P.C.Gunnell, E.Le Bihan, Y.V.Talbot, R.Henley, A.T.Johnson, L.D.Hayes, A.Bright, M.D.Raynaud, F.I.Meniconi, M.Burke, R.van Montfort, R.L.M.Rossanese, O.W.Bellenie, B.R.Hoelder, S.

(2021) J Med Chem 64: 17079-17097

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00946
  • Primary Citation of Related Structures:  
    7OKD, 7OKE, 7OKF, 7OKG, 7OKH, 7OKI, 7OKJ, 7OKK, 7OKL, 7OKM

  • PubMed Abstract: 

    We describe the optimization of modestly active starting points to potent inhibitors of BCL6 by growing into a subpocket, which was occupied by a network of five stably bound water molecules. Identifying potent inhibitors required not only forming new interactions in the subpocket but also perturbing the water network in a productive, potency-increasing fashion while controlling the physicochemical properties. We achieved this goal in a sequential manner by systematically probing the pocket and the water network, ultimately achieving a 100-fold improvement of activity. The most potent compounds displaced three of the five initial water molecules and formed hydrogen bonds with the remaining two. Compound 25 showed a promising profile for a lead compound with submicromolar inhibition of BCL6 in cells and satisfactory pharmacokinetic (PK) properties. Our work highlights the importance of finding productive ways to perturb existing water networks when growing into solvent-filled protein pockets.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein128Homo sapiensMutation(s): 0 
Gene Names: BCL6BCL5LAZ3ZBTB27ZNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens)
Explore P41182 
Go to UniProtKB:  P41182
PHAROS:  P41182
GTEx:  ENSG00000113916 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41182
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-TRP-VAL-ILE-PRO-ALA6synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VHZ (Subject of Investigation/LOI)
Query on VHZ

Download Ideal Coordinates CCD File 
D [auth A](2R)-2-[[6-[(2-chloranyl-3-cyano-pyridin-4-yl)amino]-2-oxidanylidene-1H-quinolin-4-yl]amino]-N-methyl-propanamide
C19 H17 Cl N6 O2
CWFHDWACYRWCLF-SNVBAGLBSA-N
VHN (Subject of Investigation/LOI)
Query on VHN

Download Ideal Coordinates CCD File 
C [auth A](2S)-2-[[6-[(2-chloranyl-3-cyano-pyridin-4-yl)amino]-2-oxidanylidene-1H-quinolin-4-yl]amino]-N-methyl-propanamide
C19 H17 Cl N6 O2
CWFHDWACYRWCLF-JTQLQIEISA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
VHN BindingDB:  7OKJ IC50: min: 550, max: 2670 (nM) from 2 assay(s)
VHZ BindingDB:  7OKJ IC50: min: 245, max: 250 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.47α = 90
b = 67.47β = 90
c = 165.49γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC309/A11566

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2021-12-22
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description