4NQN | pdb_00004nqn

Crystal Structure of the bromodomain of human BRD9 in complex with a triazolo-phthalazine ligand

PDB DOI: https://doi.org/10.2210/pdb4NQN/pdb

Classification: TRANSCRIPTION/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-11-25 Released: 2013-12-18
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.245 (Depositor), 0.240 (DCC)
R-Value Work:
0.188 (Depositor), 0.193 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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Literature

Crystal Structure of the bromodomain of human BRD9 in complex with a triazolo-phthalazine ligand

Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 14.78 kDa
Atom Count: 1,141
Modeled Residue Count: 113
Deposited Residue Count: 123
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 9	A	123	Homo sapiens	Mutation(s): 0 Gene Names: BRD9
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H8M2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y1Z Query on Y1Z 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]	2-chloro-N-[5-(3-methyl[1,2,4]triazolo[3,4-a]phthalazin-6-yl)-2-(morpholin-4-yl)phenyl]benzenesulfonamide C₂₆ H₂₃ Cl N₆ O₃ S WLUMGCPGWDQOSB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.245 (Depositor), 0.240 (DCC)
R-Value Work: 0.188 (Depositor), 0.193 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.12	α = 90
b = 48.42	β = 90
c = 69.32	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-12-18

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2013-12-18
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description