MolNFT v1 · #9228 · protein

Rational design, synthesis and crystallographic analysis of a hydroxyethylene-based HIV-1 protease inhibitor containing a heterocyclic P1'-P2' amide bond isostere

1HPS: “Rational design, synthesis and crystallographic analysis of a hydroxyethylene-based HIV-1 protease inhibitor…”. X-ray diffraction, 1 ligand (RUN), 1 pocket (best druggability 0.73). MolNFT v1 #9228 on GenesisL1: 3D structure…

PDB: 1HPS
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 protease
UniProt: P03366
Ligands: RUN
Pockets: 1 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV-1 protease	protein	99	7% helix, 55% strand	P03366

Ligands and binding sites

RUN · 2-[(1R,3S,4S)-1-benzyl-4-[N-(benzyloxycarbonyl)-L-valyl]amino-3-phenylpentyl]-4(5)-(2-methylpropionyl)imidazole · ligand · 2 copies · 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	373	0.73	0.84	38	RUN

Interfaces

1 interface between chains.

A–B · 1813 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

1HPS · Rational design, synthesis and crystallographic analysis of a hydroxyethylene-based HIV-1… · 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 P03366
Elsewhere: RCSB PDB 1HPS · PDBe 1HPS · UniProt P03366

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