6Y7L | pdb_00006y7l

Structure of the BRD9 bromodomain and TP-472

PDB DOI: https://doi.org/10.2210/pdb6Y7L/pdb

Classification: STRUCTURAL GENOMICS
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-03-01 Released: 2021-03-31
Deposition Author(s): Diaz-Saez, L., Krojer, T., Picaud, S., von Delft, F., Filippakopoulos, P., Arrowsmith, C.H., Edwards, A., Bountra, C., Huber, K.V.M.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.190 (Depositor), 0.200 (DCC)
R-Value Work:
0.163 (Depositor), 0.170 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of the BRD9 bromodomain and compound 2

Diaz-Saez, L., Krojer, T., Picaud, S., von Delft, F., Filippakopoulos, P., Arrowsmith, C.H., Edwards, A., Bountra, C., Huber, K.V.M.

To be published.

Macromolecule Content

Total Structure Weight: 14.36 kDa
Atom Count: 1,031
Modeled Residue Count: 113
Deposited Residue Count: 121
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 9	A	121	Homo sapiens	Mutation(s): 0 Gene Names: BRD9, UNQ3040/PRO9856
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H8M2 (Homo sapiens) Explore Q9H8M2 Go to UniProtKB: Q9H8M2
PHAROS: Q9H8M2 GTEx: ENSG00000028310
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H8M2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QMG (Subject of Investigation/LOI) Query on QMG 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]	3-(6-acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclopropyl-4-methylbenzamide C₂₀ H₁₉ N₃ O₂ RPBMXJHQYJLPDN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
QMG	BindingDB: 6Y7L	Kd: min: 32, max: 82 (nM) from 3 assay(s)
QMG	BindingDB: 6Y7L	IC50: 550 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.190 (Depositor), 0.200 (DCC)
R-Value Work: 0.163 (Depositor), 0.170 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.075	α = 90
b = 41.435	β = 101.72
c = 29.681	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Innovative Medicines Initiative		--

Revision History (Full details and data files)

Version 1.0: 2021-03-31
Type: Initial release
Version 1.1: 2024-01-24
Changes: Advisory, Data collection, Database references, Refinement description