Research workbench

Discovery of new HIV protease inhibitors with potential for convenient dosing and reduced side effects: a-790742 and a-792611.

Analyse Discovery of new HIV protease inhibitors with potential for convenient dosing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S85
Type: protein
Length: 1,188 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PROTEASE/REVERSE transcriptase
UniProt: Q9QIQ7
Ligands: LK0
Pockets: 8 · best druggability 0.83

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	PROTEASE/REVERSE transcriptase	protein	99	7% helix, 56% strand	Q9QIQ7

Ligands and binding sites

LK0 · methyl N-[(2S)-1-[[(2S,3S,5S)-5-[[(2S)-2-(methoxycarbonylamino)-3,3-dimethyl-butanoyl]amino]-3-oxidanyl-6-phenyl-1-(4-pyridin-3-ylphenyl)hexan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate · ligand · 6 copies · chains A, B, C, E, F, D, G, H, K, L, I, J

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1131	0.83	0.84	110	LK0
2	606	0.73	0.80	54	LK0
3	396	0.73	0.83	38	LK0
4	408	0.72	0.82	37	LK0
5	387	0.71	0.82	36	LK0

Interfaces

17 interfaces between chains.

I–J · 1879 Å² buried · 40 hydrogen bonds · protein-protein
K–L · 1878 Å² buried · 45 hydrogen bonds · protein-protein
G–H · 1865 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 1844 Å² buried · 42 hydrogen bonds · protein-protein
C–D · 1839 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

3S85 · Discovery of New HIV Protease Inhibitors with Potential for Convenient Dosing and Reduced… · 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 Q9QIQ7
Elsewhere: RCSB PDB 3S85 · PDBe 3S85 · UniProt Q9QIQ7

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