MolNFT v1 · #127436 · protein

Crystal structure of the human BRPF1 bromodomain in complex with BZ089

5MWH · Peregrin: “Crystal structure of the human BRPF1 bromodomain in complex with BZ089”. X-ray diffraction, 2 ligands (UWX, NO3), 4 pockets (best druggability 0.76). MolNFT v1 #127436 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5MWH
Type: protein
Length: 224 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peregrin
UniProt: P55201
Ligands: UWX, NO3
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 64% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peregrin	protein	112	64% helix, 0% strand	P55201

Ligands and binding sites

UWX · ~{N}-[1,4-dimethyl-7-morpholin-4-yl-2,3-bis(oxidanylidene)quinoxalin-6-yl]-4-(2-methylpropyl) benzenesulfonamide · ligand · 2 copies · chains A, B
NO3 · Nitrate ion · ion · 2 copies · chains B, A

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

Pockets

4 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	601	0.76	0.83	54	NO3
2	85	0.48	0.82	20	UWX
3	75	0.46	0.81	16	UWX
4	90	0.33	0.73	18	empty

Interfaces

1 interface between chains.

A–B · 571 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5MWH · Crystal structure of the human BRPF1 bromodomain in complex with BZ089 · the same entry in another collection · chain A against A, TM-score 1.00
P55201 · AlphaFold monomer V2.0 prediction for peregrin (P55201) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P55201
Elsewhere: RCSB PDB 5MWH · PDBe 5MWH · UniProt P55201

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