MolNFT v1 · #27482 · protein

HIV-1 protease in complex with pyrrolidinmethanamine

1XL2 · Protease retropepsin: “HIV-1 protease in complex with pyrrolidinmethanamine”. X-ray diffraction, 2 ligands (189, CL), 1 pocket (best druggability 0.73). MolNFT v1 #27482 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1XL2
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease retropepsin
EC: 3.4.23.16
UniProt: P03367
Ligands: 189, CL
Pockets: 1 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protease retropepsin (EC 3.4.23.16)	protein	99	4% helix, 54% strand	P03367

Ligands and binding sites

189 · N-benzyl-2-(2,6-dimethylphenoxy)-N-[((3R,4S)-4-{[isobutyl(phenylsulfonyl)amino]methyl}pyrrolidin-3-yl)methyl]acetamide · ligand · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · chains 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	548	0.73	0.81	37	189

Interfaces

1 interface between chains.

A–B · 1738 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

1XL2 · HIV-1 Protease in complex with pyrrolidinmethanamine · 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 P03367
Elsewhere: RCSB PDB 1XL2 · PDBe 1XL2 · UniProt P03367

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.