MolNFT v1 · #171108 · protein

Human BRD2(BD2) L383V mutant in complex with et-JQ1-ome

6YTM · Bromodomain-containing protein 2: “Human BRD2(BD2) L383V mutant in complex with et-JQ1-ome”. X-ray diffraction, 2 ligands (PMW, PXN), 6 pockets (best druggability 0.52). MolNFT v1 #171108 on GenesisL1: 3D structure, binding sites…

PDB: 6YTM
Type: protein
Length: 218 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2
UniProt: P25440
Ligands: PMW, PXN
Pockets: 6 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 2	protein	110	69% helix, 0% strand	P25440
B	Bromodomain-containing protein 2	protein	108	68% helix, 0% strand	P25440

Ligands and binding sites

PMW · Methyl (R)-2-((S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)butanoate · ligand · 2 copies · chains A, B
PXN · (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	114	0.52	0.81	21	PMW
2	135	0.51	0.80	21	PMW
3	153	0.42	0.74	26	empty
4	116	0.39	0.75	18	empty
5	50	0.33	0.78	11	empty

Interfaces

1 interface between chains.

A–B · 769 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6YTM · Human Brd2(BD2) L383V mutant in complex with ET-JQ1-OMe · the same entry in another collection · chain A against A, TM-score 1.00
P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P25440
Elsewhere: RCSB PDB 6YTM · PDBe 6YTM · UniProt P25440

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