4ZQL

Crystal structure of TRIM24 with 3,4-dimethoxy-N-(6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)benzenesulfonamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4ZQL/pdb

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


• Deposited: 2015-05-10 Released: 2015-06-17 
• Deposition Author(s): Tallant, C., Structural Genomics Consortium (SGC), Clark, P.G.K., Vieira, L.C.C., Krojer, T., Nunez-Alonso, G., Picaud, S., Fedorov, O., Dixon, D.J., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.199 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

Crystal structure of TRIM24 with 3,4-dimethoxy-N-(6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)benzenesulfonamide inhibitor

Clark, P.G., Vieira, L.C., Tallant, C., Fedorov, O., Singleton, D.C., Rogers, C.M., Monteiro, O.P., Bennett, J.M., Baronio, R., Muller, S., Daniels, D.L., Mendez, J., Knapp, S., Brennan, P.E., Dixon, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.08 kDa 
• Atom Count: 3,145 
• Modelled Residue Count: 353 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription intermediary factor 1-alpha	A, B	184	Homo sapiens	Mutation(s): 0  Gene Names: TRIM24, RNF82, TIF1, TIF1A 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4QH	I [auth B]	3,4-dimethoxy-N-[6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl]benzenesulfonamide C24 H25 N3 O7 S KNVIUMWNYXDULF-UHFFFAOYSA-N
1PE	K [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
SO4	E [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4QH	BindingDB:  4ZQL	Kd: 222 (nM) from 1 assay(s)
		IC50: min: 430, max: 750 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.199 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.414	α = 90
b = 36.661	β = 109.87
c = 128.989	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Tallant, C., Structural Genomics Consortium (SGC), Clark, P.G.K., Vieira, L.C.C., Krojer, T., Nunez-Alonso, G., Picaud, S., Fedorov, O., Dixon, D.J., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Knapp, S.

Revision History  

• Version 1.0: 2015-06-17
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description