8QB2

Crystal Structure of BRPF1 bromodomain in complex with acetyl-pyrrole derivative compound 79

PDB DOI: https://doi.org/10.2210/pdb8QB2/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-08-24 Released: 2024-09-11
Deposition Author(s): Dalle Vedove, A., Cazzanelli, G., Lolli, G.
Funding Organization(s): Italian Association for Cancer Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 ?
R-Value Free:
0.196 (Depositor), 0.197 (DCC)
R-Value Work:
0.168 (Depositor), 0.169 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Dual BET/BRPF1 inhibitors induce morphological alteration and cellular death in various human cancer cell lines

Cazzanelli, G., Dalle Vedove, A., Caflisch, A., Lolli, G.

To be published.

Macromolecule Content

Total Structure Weight: 14.13 kDa
Atom Count: 1,092
Modelled Residue Count: 112
Deposited Residue Count: 116
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55201
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GKI (Subject of Investigation/LOI) Query on GKI Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-[2-methyl-4-(3-methylbutyl)-5-(2-piperazin-1-yl-1,3-thiazol-4-yl)-1~{H}-pyrrol-3-yl]ethanone C₁₉ H₂₈ N₄ O S FEVXGFVVUGZYTO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 ?
R-Value Free: 0.196 (Depositor), 0.197 (DCC)
R-Value Work: 0.168 (Depositor), 0.169 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 60.49	α = 90
b = 60.49	β = 90
c = 62.234	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Dalle Vedove, A.

Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	MFAG 2017 - ID. 19882

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.