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- PDB-9oob: Crystal structure of MYST acetyltransferase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9oob
TitleCrystal structure of MYST acetyltransferase domain in complex with inhibitor 8
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE/INHIBITOR / Acetyltransferase / Inhibitor / Complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / dosage compensation by inactivation of X chromosome ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / dosage compensation by inactivation of X chromosome / post-embryonic hemopoiesis / myeloid cell differentiation / NSL complex / negative regulation of epithelial to mesenchymal transition / negative regulation of type I interferon production / oogenesis / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / MLL1 complex / histone acetyltransferase complex / protein-lysine-acetyltransferase activity / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase / neurogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / kinetochore / regulation of autophagy / nuclear matrix / HATs acetylate histones / chromosome / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain ...: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsHermans, S.J. / Suwandi, A. / Parker, M.W. / Baell, J.B.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1030704 Australia
National Health and Medical Research Council (NHMRC, Australia)1080146 Australia
National Health and Medical Research Council (NHMRC, Australia)1117602 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1194263 Australia
CitationJournal: J.Med.Chem. / Year: 2026
Title: Biological Activity and Structural Biology of Current KAT6A Inhibitor Chemotypes.
Authors: Suwandi, A. / Jin, J. / Zhao, Y. / Mudududdla, R. / Gee, Y.S. / Deora, G.S. / Sun, Y. / Wei, H. / Huang, F. / He, J.S. / George, A.J. / Hermans, S.J. / Leaver, D.J. / Parker, M.W. / Baell, J.B.
History
DepositionMay 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2619
Polymers34,4341
Non-polymers8278
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.545, 58.623, 120.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone acetyltransferase KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 34433.598 Da / Num. of mol.: 1 / Mutation: A142S, L145M, T146I, K157R, S204W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1, PP7073 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7Z6, histone acetyltransferase

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Non-polymers , 6 types, 324 molecules

#2: Chemical ChemComp-A1CDK / 6-(azetidin-1-yl)-N-(2-ethoxy-6-methoxybenzene-1-sulfonyl)-4-fluoro-1-benzofuran-2-carboxamide


Mass: 448.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21FN2O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris pH 7.0, 0.25 M MgCl2, 8% PEG8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953725305062 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725305062 Å / Relative weight: 1
ReflectionResolution: 1.83→34.88 Å / Num. obs: 56088 / % possible obs: 99.88 % / Redundancy: 7.8 % / Biso Wilson estimate: 24.38 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.0254 / Rrim(I) all: 0.0715 / Net I/σ(I): 20.38
Reflection shellResolution: 1.83→1.89 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.91 / Num. unique obs: 2900 / CC1/2: 0.855 / CC star: 0.96 / Rpim(I) all: 0.2588 / Rrim(I) all: 0.737 / % possible all: 99.28

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→34.88 Å / SU ML: 0.1704 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9735
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2076 2705 4.82 %
Rwork0.1766 53383 -
obs0.1781 56088 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.48 Å2
Refinement stepCycle: LAST / Resolution: 1.83→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 48 316 2583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882334
X-RAY DIFFRACTIONf_angle_d0.99873160
X-RAY DIFFRACTIONf_chiral_restr0.064326
X-RAY DIFFRACTIONf_plane_restr0.0076391
X-RAY DIFFRACTIONf_dihedral_angle_d13.1687315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.860.2961390.29062768X-RAY DIFFRACTION97.91
1.86-1.90.27941180.2512822X-RAY DIFFRACTION100
1.9-1.940.2521330.23092827X-RAY DIFFRACTION100
1.94-1.980.24791410.22072783X-RAY DIFFRACTION99.97
1.98-2.020.25381450.20872881X-RAY DIFFRACTION99.97
2.02-2.070.24991280.19962784X-RAY DIFFRACTION100
2.07-2.130.23311630.19512783X-RAY DIFFRACTION100
2.13-2.190.19271560.19272814X-RAY DIFFRACTION99.97
2.19-2.260.20261420.18062803X-RAY DIFFRACTION99.97
2.26-2.340.22421240.1882858X-RAY DIFFRACTION99.9
2.35-2.440.24521340.18912822X-RAY DIFFRACTION99.93
2.44-2.550.21931460.18262773X-RAY DIFFRACTION99.97
2.55-2.680.18181400.18492830X-RAY DIFFRACTION100
2.68-2.850.20431270.17822806X-RAY DIFFRACTION100
2.85-3.070.19511780.16992824X-RAY DIFFRACTION99.97
3.07-3.380.18311500.16572782X-RAY DIFFRACTION99.97
3.38-3.870.19031470.14452825X-RAY DIFFRACTION100
3.87-4.870.19521510.13822780X-RAY DIFFRACTION99.83
4.87-34.880.20281430.18572818X-RAY DIFFRACTION99.9

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