9MJG | pdb_00009mjg

Crystal structure of HAT1 in complex with XS380871


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 
    0.270 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.236 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Enantioselective protein affinity selection mass spectrometry (E-ASMS).

Wang, X.Sun, J.Ahmad, S.Yang, D.Li, F.Chan, U.H.Zeng, H.Simoben, C.V.Green, S.R.Silva, M.Houliston, S.Dong, A.Bolotokova, A.Gibson, E.Kutera, M.Ghiabi, P.Kondratov, I.Matviyuk, T.Chuprina, A.Mavridi, D.Lenz, C.Joerger, A.C.Brown, B.D.Heath, R.B.Yue, W.W.Robbie, L.K.Beyett, T.S.Muller, S.Knapp, S.Owen, D.R.Harding, R.Schapira, M.Brown, P.J.Santhakumar, V.Ackloo, S.Arrowsmith, C.H.Edwards, A.M.Peng, H.Halabelian, L.

(2025) Nat Commun 17: 651-651

  • DOI: https://doi.org/10.1038/s41467-025-67403-2
  • Primary Citation of Related Structures:  
    9MJG

  • PubMed Abstract: 

    We report an enantioselective protein affinity selection mass spectrometry screening approach (E-ASMS) that enables the detection of weak binders, informs on selectivity, and generates orthogonal confirmation of binding. After method development with control proteins, we screen 31 human proteins against a designed library of 8,217 chiral compounds. We identify 16 binders to 12 targets, including many proteins predicted to be "challenging to ligand", and confirm their interactions through orthogonal biophysical assays. Seven binders to six targets display enantioselective binding, with K D values ranging from 3 to 20 µM. Binders for four targets (DDB1, WDR91, WDR55, and HAT1) are selected for in-depth characterization using X-ray crystallography. In all four cases, the mechanisms underlying enantioselectivity are readily explained. These results demonstrate that E-ASMS enables the identification and characterization of selective and weakly binding ligands for novel protein targets with unprecedented throughput and sensitivity.


  • Organizational Affiliation
    • Department of Chemistry, University of Toronto, Toronto, ON, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase type B catalytic subunit
A, B, C, D, E
A, B, C, D, E, F, G, H
322Homo sapiensMutation(s): 0 
Gene Names: HAT1hCG_16790
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O14929 (Homo sapiens)
Explore O14929 
Go to UniProtKB:  O14929
PHAROS:  O14929
GTEx:  ENSG00000128708 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14929
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BLX (Subject of Investigation/LOI)
Query on A1BLX

Download Ideal Coordinates CCD File 
I [auth A]
J [auth B]
K [auth C]
L [auth D]
M [auth E]
I [auth A],
J [auth B],
K [auth C],
L [auth D],
M [auth E],
N [auth F],
O [auth G],
P [auth H]
(4S,7R)-4-(3-ethoxy-4-hydroxy-5-nitrophenyl)-7-(4-fluorophenyl)-4,6,7,8-tetrahydroquinoline-2,5(1H,3H)-dione
C23 H21 F N2 O6
ZIQMAORRANWURA-CJNGLKHVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free:  0.270 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.236 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.889α = 84.376
b = 87.838β = 80.069
c = 118.029γ = 76.763
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Database references