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Design, activity and 2.8 ångströms crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease

Analyse Design, activity and 2.8 ångströms crystal structure of a C2 symmetric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 9HVP
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 protease
Ligands: 0E9
Pockets: 1 · best druggability 0.71

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV-1 protease	protein	99	4% helix, 49% strand	—

Ligands and binding sites

0E9 · benzyl [(1R,4S,6S,9R)-4,6-dibenzyl-5-hydroxy-1,9-bis(1-methylethyl)-2,8,11-trioxo-13-phenyl-12-oxa-3,7,10-triazatridec-1-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	345	0.71	0.83	34	0E9

Interfaces

1 interface between chains.

A–B · 1824 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

9HVP · Design, activity and 2.8 Angstroms crystal structure of a C2 symmetric inhibitor… · 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
Elsewhere: RCSB PDB 9HVP · PDBe 9HVP

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