MolNFT v1 · #140851 · protein

Crystal structure of zika virus NS3 protease in complex with a dipeptide inhibitor

5YOF · NS2B cofactor: “Crystal structure of zika virus NS3 protease in complex with a dipeptide inhibitor”. X-ray diffraction, 1 ligand (7HS), 1 pocket (best druggability 0.38). MolNFT v1 #140851 on GenesisL1: 3D structure, binding sites…

PDB: 5YOF
Type: protein
Length: 195 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NS2B cofactor; NS3 protease
Ligands: 7HS
Pockets: 1 · best druggability 0.38

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NS2B cofactor	protein	39	0% helix, 46% strand	—
B	NS3 protease	protein	156	4% helix, 46% strand	—

Ligands and binding sites

7HS · (S)-2-acetamido-6-amino-N-((S)-5-guanidino-1-oxopentan-2-yl)hexanamide · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	116	0.38	0.74	22	empty

Interfaces

1 interface between chains.

A–B · 2017 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5YOF · Crystal structure of zika virus NS3 protease in complex with a dipeptide 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 5YOF · PDBe 5YOF

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