MolNFT v1 · #115599 · protein

X-ray crystal structure of wild type HIV-1 protease in complex with grl-0476

5COK: “X-ray crystal structure of wild type HIV-1 protease in complex with grl-0476”. X-ray diffraction, 1 ligand (52U), 2 pockets (best druggability 0.72). MolNFT v1 #115599 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5COK
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 protease
UniProt: G0X8E3
Ligands: 52U
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV-1 protease	protein	99	4% helix, 52% strand	G0X8E3

Ligands and binding sites

52U · (3aS,4S,7aR)-hexahydro-4H-furo[2,3-b]pyran-4-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate · ligand · chains A, B

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

Pockets

2 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	353	0.72	0.84	34	52U
2	80	0.46	0.81	14	empty

Interfaces

1 interface between chains.

A–B · 1718 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

5COK · X-ray crystal structure of wild type HIV-1 protease in complex with GRL-0476 · 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 G0X8E3
Elsewhere: RCSB PDB 5COK · PDBe 5COK · UniProt G0X8E3

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