MolNFT v1 · #159704 · protein

X-ray crystal structure of wild type HIV-1 protease in complex with grl-004

6OYD: “X-ray crystal structure of wild type HIV-1 protease in complex with grl-004”. X-ray diffraction, 1 ligand (NKA), 2 pockets (best druggability 0.47). MolNFT v1 #159704 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OYD
Type: protein
Length: 99 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
UniProt: Q8ULI2
Ligands: NKA
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protease	protein	99	4% helix, 49% strand	Q8ULI2

Ligands and binding sites

NKA · (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl {(2S,3R)-1-(4-fluorophenyl)-3-hydroxy-4-[(2-methylpropyl)({2-[(propan-2-yl)amino]-1,3-benzoxazol-6-yl}sulfonyl)amino]butan-2-yl}carbamate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	157	0.47	0.76	20	empty
2	80	0.31	0.73	19	empty

Compared structures

6OYD · X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004 · 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 Q8ULI2
Elsewhere: RCSB PDB 6OYD · PDBe 6OYD · UniProt Q8ULI2

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