5FG4 | pdb_00005fg4

Crystal structure of the bromodomain of human BRPF1 in complex with OF-1 chemical probe

• PDB DOI: https://doi.org/10.2210/pdb5FG4/pdb

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


• Deposited: 2015-12-20 Released: 2016-01-13 
• Deposition Author(s): Tallant, C., Owen, D.R., Gerstenberger, B.S., Savitsky, P., Chaikuad, A., Fedorov, O., Nunez-Alonso, G., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Knapp, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the bromodomain of human BRPF1 in complex with OF-1 chemical probe

Tallant, C., Owen, D.R., Gerstenberger, B.S., Savitsky, P., Chaikuad, A., Fedorov, O., Nunez-Alonso, G., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Knapp, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.14 kDa 
• Atom Count: 1,037 
• Modeled Residue Count: 113 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peregrin	A	116	Homo sapiens	Mutation(s): 0  Gene Names: BRPF1, BR140
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens) Explore P55201  Go to UniProtKB:  P55201
PHAROS:  P55201 GTEx:  ENSG00000156983

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5XE	B [auth A]	4-bromanyl-~{N}-(6-methoxy-1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)-2-methyl-benzenesulfonamide C17 H18 Br N3 O4 S YUNQZQREIHWDQT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5XE	BindingDB:  5FG4	Kd: 100 (nM) from 1 assay(s)
		IC50: min: 270, max: 383 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.802	α = 90
b = 60.704	β = 100.43
c = 51.171	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Tallant, C., Owen, D.R., Gerstenberger, B.S., Savitsky, P., Chaikuad, A., Fedorov, O., Nunez-Alonso, G., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Knapp, S.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description