9FKR | pdb_00009fkr

KAT6A IN COMPLEX WITH SMALL MOLECULE INHIBITOR BAY-184


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.238 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery and Characterization of BAY-184: A New Potent and Selective Acylsulfonamide-Benzofuran In Vivo -Active KAT6AB Inhibitor.

Ter Laak, A.Hillig, R.C.Ferrara, S.J.Korr, D.Barak, N.Lienau, P.Herbert, S.Fernandez-Montalvan, A.E.Neuhaus, R.Gorjanacz, M.Puetter, V.Badock, V.Bone, W.Strathdee, C.Siegel, F.Schatz, C.Nowak-Reppel, K.Doehr, O.Gradl, S.Hartung, I.V.Meyerson, M.Bouche, L.

(2024) J Med Chem 67: 19282-19303

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01709
  • Primary Citation Related Structures: 
    9FKR

  • PubMed Abstract: 

    KAT6A and KAT6B genes are two closely related lysine acetyltransferases that transfer an acetyl group from acetyl coenzyme A (AcCoA) to lysine residues of target histone substrates, hence playing a key role in chromatin regulation. KAT6A and KAT6B genes are frequently amplified in various cancer types. In breast cancer, the 8p11-p12 amplicon occurs in 12-15% of cases, resulting in elevated copy numbers and expression levels of chromatin modifiers like KAT6A. Here, we report the discovery of a new acylsulfonamide-benzofuran series as a novel structural class for KAT6A/B inhibition. These compounds were identified through high-throughput screening and subsequently optimized using molecular modeling and cocrystal structure determination. The final tool compound, BAY-184 ( 29 ), was successfully validated in an in vivo proof-of-concept study.


  • Organizational Affiliation
    • Bayer AG, Pharmaceuticals, Research and Development, Müllerstrasse 178, Berlin 13353, Germany.

Macromolecule Content 

  • Total Structure Weight: 65.79 kDa 
  • Atom Count: 4,487 
  • Modeled Residue Count: 523 
  • Deposited Residue Count: 544 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone acetyltransferase KAT6A
A, B
272Homo sapiensMutation(s): 4 
Gene Names: KAT6AMOZMYST3RUNXBP2ZNF220
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q92794 (Homo sapiens)
Explore Q92794 
Go to UniProtKB:  Q92794
PHAROS:  Q92794
GTEx:  ENSG00000083168 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92794
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IDR

Query on A1IDR



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
6-(dimethylamino)-~{N}-(2-phenylphenyl)sulfonyl-1-benzofuran-2-carboxamide
C23 H20 N2 O4 S
ZUWIDJYXRPTMQW-UHFFFAOYSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
A, B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.238 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.805α = 92.22
b = 59.921β = 90.82
c = 65.85γ = 103.2
Software Package:
Software NamePurpose
REFMACrefinement
pointlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Database references