25VX | pdb_000025vx

Crystal Structure of MYST histone acetyltransferase KAT6A in complex with inhibitor Compound 9

PDB DOI: https://doi.org/10.2210/pdb25VX/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2026-04-20 Released: 2026-05-06
Deposition Author(s): NarasimhaRao, K., Vijayshankar, N., SumalathaRani, T., Kalishankar, B., Chandregowda, V., Chandrasekar, A., Susanta, S., Raymond, A.N., David, C.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.266 (Depositor), 0.259 (DCC)
R-Value Work:
0.199 (Depositor), 0.207 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of MYST histone acetyltransferase KAT6A in complex with Compound 9

NarasimhaRao, K., Vijayshankar, N., SumalathaRani, T., Kalishankar, B., Chandregowda, V., Chandrasekar, A., Susanta, S., Raymond, A.N., David, C.M.

To be published.

Macromolecule Content

Total Structure Weight: 32.41 kDa
Atom Count: 2,315
Modeled Residue Count: 266
Deposited Residue Count: 271
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase KAT8	A	271	Homo sapiens	Mutation(s): 6 Gene Names: KAT8, MOF, MYST1, PP7073 EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7Z6 (Homo sapiens) Explore Q9H7Z6 Go to UniProtKB: Q9H7Z6
PHAROS: Q9H7Z6 GTEx: ENSG00000103510
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H7Z6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1MGC Query on A1MGC Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2,6-dimethoxy-~{N}-(5-phenyl-3,4-dihydro-2~{H}-pyrano[2,3-e][1,2]benzoxazol-9-yl)benzenesulfonamide C₂₄ H₂₂ N₂ O₆ S VWDAWCBPOODBJV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	A	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.266 (Depositor), 0.259 (DCC)
R-Value Work: 0.199 (Depositor), 0.207 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.19	α = 90
b = 57.622	β = 90
c = 122.036	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

NarasimhaRao, K.

Vijayshankar, N.

SumalathaRani, T.

Kalishankar, B.

Chandregowda, V.

Chandrasekar, A.

Funding Organization	Location	Grant Number
Not funded	India	--

Revision History (Full details and data files)

Version 1.0: 2026-05-06
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.