MolNFT v1 · #118898 · protein

Crystal structure of the bromodomain of human BRPF1 in complex with a benzimidazole ligand

5FFY · Peregrin: “Crystal structure of the bromodomain of human BRPF1 in complex with a benzimidazole ligand”. X-ray diffraction, 1 ligand (5XD), 1 pocket (best druggability 0.50). MolNFT v1 #118898 on GenesisL1: 3D structure, binding…

PDB: 5FFY
Type: protein
Length: 111 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peregrin
UniProt: P55201
Ligands: 5XD
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peregrin	protein	111	65% helix, 0% strand	P55201

Ligands and binding sites

5XD · 4-ethyl-~{N}-(6-methoxy-1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)benzenesulfonamide · ligand · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.50	0.83	18	5XD

Compared structures

5FFY · Crystal structure of the bromodomain of human BRPF1 in complex with a benzimidazole ligand · 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 0.97

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

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