9GDG | pdb_00009gdg

Crystal structure of TRIM24 PHD-BRD in complex with N-(2-(2-(2-acetamidoethoxy)ethoxy)ethyl)-3-(N-(1,3-dimethyl-2-oxo-6-(3-propoxyphenoxy)-2,3-dihydro-1H-benzo[d]imidazol-5-yl)sulfamoyl)benzamide (PEG linker unresolved)

PDB DOI: https://doi.org/10.2210/pdb9GDG/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-05 Released: 2025-08-13
Deposition Author(s): Platt, M.A., Kot, E., Conway, S.J., Koekemoer, L.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.210 (Depositor), 0.212 (DCC)
R-Value Work:
0.150 (Depositor), 0.158 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of TRIM24 PHD-BRD in complex with N-(2-(2-(2-acetamidoethoxy)ethoxy)ethyl)-3-(N-(1,3-dimethyl-2-oxo-6-(3-propoxyphenoxy)-2,3-dihydro-1H-benzo[d]imidazol-5-yl)sulfamoyl)benzamide (PEG linker unresolved)

Platt, M.A., Kot, E., Conway, S.J., Koekemoer, L.

To be published.

Macromolecule Content

Total Structure Weight: 22.3 kDa
Atom Count: 1,599
Modeled Residue Count: 176
Deposited Residue Count: 185
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription intermediary factor 1-alpha	A [auth B]	185	Homo sapiens	Mutation(s): 0 Gene Names: TRIM24, RNF82, TIF1, TIF1A EC: 2.3.2.27
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15164
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IKF (Subject of Investigation/LOI) Query on A1IKF Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	N-(2-(2-(2-acetamidoethoxy)ethoxy)ethyl)-3-(N-(1,3-dimethyl-2-oxo-6-(3-propoxyphenoxy)-2,3-dihydro-1H-benzo[d]imidazol-5-yl)sulfamoyl)benzamide C₃₃ H₄₁ N₅ O₉ S RIAWPTKWSYPUDU-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B]	C [auth B], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.210 (Depositor), 0.212 (DCC)
R-Value Work: 0.150 (Depositor), 0.158 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.942	α = 90
b = 36.652	β = 111.325
c = 65.456	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
STARANISO	data scaling
PHASER	phasing
autoPROC	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T008784/1

Revision History (Full details and data files)

Version 1.0: 2025-08-13
Type: Initial release

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