5H1V | pdb_00005h1v

Complex structure of TRIM24 PHD-bromodomain and inhibitor 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.220 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The polar warhead of a TRIM24 bromodomain inhibitor rearranges a water-mediated interaction network

Liu, J.Li, F.Bao, H.Jiang, Y.Zhang, S.Ma, R.Gao, J.Wu, J.Ruan, K.

(2017) FEBS J 284: 1082-1095

  • DOI: https://doi.org/10.1111/febs.14041
  • Primary Citation Related Structures: 
    5H1T, 5H1U, 5H1V

  • PubMed Abstract: 

    Tripartite motif-containing protein 24 (TRIM24) is closely correlated with multiple cancers, and a recent study demonstrated that the bromodomain of TRIM24 is essential for the proliferation of lethal castration-resistant prostate cancer. Here, we identify three new inhibitors of the TRIM24 bromodomain using NMR fragment-based screening. The crystal structures of two new inhibitors in complex with the TRIM24 bromodomain reveal that the water-bridged interaction network is conserved in the same fashion as those for known benzoimidazolone inhibitors. Interestingly, the polar substitution on the warhead of one new inhibitor pulls the whole ligand approximately 2 Å into the inner side pocket of the TRIM24 bromodomain, and thus exhibits a binding mode significantly different from other known bromodomain ligands. This mode provides a useful handle for further hit-to-lead evolution toward novel inhibitors of the TRIM24 bromodomain. Structural data are available in the PDB under the accession numbers 5H1T, 5H1U, and 5H1V.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China.

Macromolecule Content 

  • Total Structure Weight: 43.25 kDa 
  • Atom Count: 2,941 
  • Modeled Residue Count: 339 
  • Deposited Residue Count: 366 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription intermediary factor 1-alpha
A, B
183Homo sapiensMutation(s): 0 
Gene Names: TRIM24RNF82TIF1TIF1A
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O15164 (Homo sapiens)
Explore O15164 
Go to UniProtKB:  O15164
PHAROS:  O15164
GTEx:  ENSG00000122779 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15164
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7FU

Query on 7FU



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
2-Hydrazino-1,3-benzothiazole-6-carbohydrazide
C8 H9 N5 O S
JTWKTGKIUURTLG-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
F [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
G [auth B],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.220 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.028α = 90
b = 36.027β = 96.88
c = 113.207γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing
HKLdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-02-22 
  • Deposition Author(s): Liu, J.

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-04-19
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Data collection
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description