MolNFT v1 · #135365 · protein

Crystal structure of BRD9 bromodomain

5TWX · Bromodomain-containing protein 9: “Crystal structure of BRD9 bromodomain”. X-ray diffraction, 1 ligand (7P7), 3 pockets (best druggability 0.65). MolNFT v1 #135365 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5TWX
Type: protein
Length: 442 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 9
UniProt: Q9H8M2
Ligands: 7P7
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 62% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 9	protein	114	59% helix, 0% strand	Q9H8M2
B	Bromodomain-containing protein 9	protein	111	63% helix, 0% strand	Q9H8M2
C	Bromodomain-containing protein 9	protein	108	63% helix, 0% strand	Q9H8M2
D	Bromodomain-containing protein 9	protein	109	62% helix, 0% strand	Q9H8M2

Ligands and binding sites

7P7 · N-[6-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)hexyl]-2-(4-{2-[N-(1,1-dioxo-1lambda~6~-thian-4-yl)carbamimidoyl]-5-methyl-4-oxo-4,5-dihydrothieno[3,2-c]pyridin-7-yl}-2-methoxyphenoxy)acetamide · ligand · 4 copies · chains A, C, B, D

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	323	0.65	0.80	43	7P7
2	319	0.64	0.80	41	7P7
3	71	0.53	0.86	20	empty

Interfaces

4 interfaces between chains.

A–B · 825 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 534 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 275 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 237 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5TWX · Crystal Structure of BRD9 bromodomain · the same entry in another collection · chain D against D, TM-score 1.00
Q9H8M2 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 9 (Q9H8M2) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 5TWX · PDBe 5TWX · UniProt Q9H8M2

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