MolNFT v1 · #118468 · protein

Crystal structure of the BRD9 bromodomain in complex with compound 3.

5F2P: “Crystal structure of the BRD9 bromodomain in complex with compound 3.”. X-ray diffraction, 1 ligand (5TY), 2 pockets (best druggability 0.55). MolNFT v1 #118468 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5F2P
Type: protein
Length: 226 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BRD9
UniProt: Q9H8M2
Ligands: 5TY
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 63% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	BRD9	protein	113	63% helix, 0% strand	Q9H8M2

Ligands and binding sites

5TY · 2-(dimethylamino)-6-methyl-pyrido[4,3-d]pyrimidin-5-one · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	78	0.55	0.86	16	5TY
2	78	0.46	0.81	17	5TY

Interfaces

1 interface between chains.

A–B · 922 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5F2P · Crystal structure of the BRD9 bromodomain in complex with compound 3. · the same entry in another collection · chain A against A, TM-score 1.00
Q9H8M2 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 9 (Q9H8M2) · a predicted model of the same protein · chain A against A, TM-score 0.93

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9H8M2
Elsewhere: RCSB PDB 5F2P · PDBe 5F2P · UniProt Q9H8M2

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