MolNFT v1 · #116538 · protein

Crystal structure of HIV-1 protease inhibitors containing substituted fused-tetrahydropyranyl tetrahydrofuran as P2-ligand grl-004-11A

5DGU · Pol protein: “Crystal structure of HIV-1 protease inhibitors containing substituted fused-tetrahydropyranyl tetrahydrofuran…”. X-ray diffraction, 3 ligands (5B7, NA, CL), 1 pocket (best druggability 0.72). MolNFT v1 #116538 on…

PDB: 5DGU
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pol protein
UniProt: Q8Q3H0
Ligands: 5B7, NA, CL
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pol protein	protein	99	7% helix, 56% strand	Q8Q3H0

Ligands and binding sites

5B7 · (3r,3ar,4s,7as)-3-methoxyhexahydro-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
NA · Sodium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 3 copies · chains A, B
ACT · Acetate ion · additive · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	415	0.72	0.83	41	5B7

Interfaces

1 interface between chains.

A–B · 1869 Å² buried · 37 hydrogen bonds · protein-protein

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 Q8Q3H0
Elsewhere: RCSB PDB 5DGU · PDBe 5DGU · UniProt Q8Q3H0

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