MolNFT v1 · #128863 · protein

Human BRD2(BD2) mutant in complex with al

5O3B · Bromodomain-containing protein 2: “Human BRD2(BD2) mutant in complex with al”. X-ray diffraction, 1 ligand (9HZ), 7 pockets (best druggability 0.85). MolNFT v1 #128863 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5O3B
Type: protein
Length: 437 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2
UniProt: P25440
Ligands: 9HZ
Pockets: 7 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 2	protein	108	70% helix, 0% strand	P25440
B, C	Bromodomain-containing protein 2	protein	110	69% helix, 0% strand	P25440
D	Bromodomain-containing protein 2	protein	109	69% helix, 0% strand	P25440

Ligands and binding sites

9HZ · Methyl (2~{R})-2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-A][1, 4]benzodiazepin-4-yl]pent-4-enoate · ligand · 4 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1129	0.85	0.86	86	empty
2	129	0.53	0.81	20	9HZ
3	139	0.52	0.80	20	9HZ
4	137	0.51	0.79	20	9HZ
5	139	0.51	0.79	21	9HZ

Interfaces

6 interfaces between chains.

A–B · 805 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 794 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 527 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 498 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 67 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5O3B · Human Brd2(BD2) mutant in complex with AL · the same entry in another collection · chain D against D, TM-score 1.00
P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain C 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 5O3B · PDBe 5O3B · UniProt P25440

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