7M16 | pdb_00007m16

Triazole-based BET family bromodomain inhibitor bound to BRD4(D1)

• PDB DOI: https://doi.org/10.2210/pdb7M16/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-12 Released: 2021-09-29 
• Deposition Author(s): Johnson, J.A., Pomerantz, W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Cancer Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Systematically Mitigating the p38alpha Activity of Triazole-based BET Inhibitors

Carlson, A.S., Cui, H., Divakaran, A., Johnson, J.A., Brunner, R.M., Pomerantz, W.C.K., Topczewski, J.J.

(2019) ACS Med Chem Lett 10: 1296-1301

• DOI: https://doi.org/10.1021/acsmedchemlett.9b00227

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.5 kDa 
• Atom Count: 1,185 
• Modeled Residue Count: 123 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YNS (Subject of Investigation/LOI)	B [auth A]	4-{5-[6-(3,5-dimethylanilino)pyridin-2-yl]-4-methyl-1H-1,2,3-triazol-1-yl}piperidine-1-carboximidamide C22 H28 N8 KEWZHLXKQSXXAR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.551	α = 90
b = 47.398	β = 90
c = 79.816	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): Johnson, J.A., Pomerantz, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM124718
American Cancer Society	United States	129819-IRG-16-189-58-IRG88

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description