MolNFT v1 · #145859 · protein

X-ray crystal structure of wild type HIV-1 protease in complex with grl-087-13

6D0D: “X-ray crystal structure of wild type HIV-1 protease in complex with grl-087-13”. X-ray diffraction, 1 ligand (FQ4), 1 pocket (best druggability 0.72). MolNFT v1 #145859 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6D0D
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
UniProt: C8B467
Ligands: FQ4
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	Protease	protein	99	7% helix, 55% strand	C8B467

Ligands and binding sites

FQ4 · (3as,4s,7ar)-hexahydro-4H-furo[2,3-b]pyran-4-yl [(2S, 3R)-1-(4-fluorophenyl)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}butan-2-yl]carbamate · 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	374	0.72	0.83	34	FQ4

Interfaces

1 interface between chains.

A–B · 1848 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

6D0D · X-ray crystal structure of wild type HIV-1 protease in complex with GRL-087-13 · 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 C8B467
Elsewhere: RCSB PDB 6D0D · PDBe 6D0D · UniProt C8B467

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