5FG6

Crystal structure of the bromodomain of human BRD1 (BRPF2) in complex with OF-1 chemical probe

PDB DOI: https://doi.org/10.2210/pdb5FG6/pdb

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

Deposited: 2015-12-20 Released: 2016-02-03
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: 1.10 Å
R-Value Free: 0.197
R-Value Work: 0.181
R-Value Observed: 0.182

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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of the bromodomain of human BRD1 (BRPF2) 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.

Macromolecule Content

Total Structure Weight: 15.7 kDa
Atom Count: 1,229
Modelled Residue Count: 118
Deposited Residue Count: 128
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 1	A	128	Homo sapiens	Mutation(s): 0 Gene Names: BRD1, BRL, BRPF2
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens) Explore O95696 Go to UniProtKB: O95696
PHAROS: O95696 GTEx: ENSG00000100425
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95696
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5XE Query on 5XE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [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		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
5XE	BindingDB: 5FG6	Kd: 500 (nM) from 1 assay(s)
5XE	BindingDB: 5FG6	IC50: min: 128, max: 1679 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.197
R-Value Work: 0.181
R-Value Observed: 0.182
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.771	α = 90
b = 84.328	β = 90
c = 52.08	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-02-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-02-03
Type: Initial release
Version 2.0: 2024-01-10
Changes: Atomic model, Data collection, Database references, Refinement description

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Help and Resources

5FG6

Crystal structure of the bromodomain of human BRD1 (BRPF2) in complex with OF-1 chemical probe

Crystal structure of the bromodomain of human BRD1 (BRPF2) in complex with OF-1 chemical probe

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)