MolNFT v1 · #1830 · protein

HIV-1 (2:31-37, 47, 82) protease complexed with inhibitor SB203386

1BDQ · HIV-1 protease: “HIV-1 (2:31-37, 47, 82) protease complexed with inhibitor SB203386”. X-ray diffraction, 1 ligand (IM1), 1 pocket (best druggability 0.72). MolNFT v1 #1830 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1BDQ
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 protease
EC: 3.4.23.16
UniProt: P04587
Ligands: IM1
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV-1 protease (EC 3.4.23.16)	protein	99	7% helix, 55% strand	P04587

Ligands and binding sites

IM1 · (2R,4S,5S,1'S)-2-phenylmethyl-4-hydroxy-5-(tert-butoxycarbonyl)amino-6-phenyl hexanoyl-N-(1'-imidazo-2-yl)-2'-methylpropanamide · ligand · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	308	0.72	0.85	36	IM1

Interfaces

1 interface between chains.

A–B · 1831 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

1BDQ · HIV-1 (2:31-37, 47, 82) protease complexed with inhibitor SB203386 · the same entry in another collection · chain A against A, TM-score 1.00

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 P04587
Elsewhere: RCSB PDB 1BDQ · PDBe 1BDQ · UniProt P04587

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