5ZMS image
Entry Detail
PDB ID:
5ZMS
Title:
Crystal structure of Zika NS3 protease in complex with 4-guanidinomethyl-phenylacetyl-Lys-Lys-Arg-H
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2018-04-05
Release Date:
2018-10-17
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.21
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Serine protease subunit NS2B
Chain IDs:A, C (auth: D), E (auth: G), G (auth: J)
Chain Length:53
Number of Molecules:4
Biological Source:Zika virus
Polymer Type:polypeptide(L)
Description:NS3 protease
Chain IDs:B, D (auth: E), F (auth: H), H (auth: K)
Chain Length:178
Number of Molecules:4
Biological Source:Zika virus (strain Mr 766)
Polymer Type:polypeptide(L)
Description:4-guanidinomethyl-phenylacetyl-Lys-Lys-Arg-H
Chain IDs:I (auth: F), J (auth: I)
Chain Length:4
Number of Molecules:2
Biological Source:synthetic construct
Peptide-like Molecules
PRD_002298
Primary Citation
Structures of Zika virus NS2B-NS3 protease in complex with peptidomimetic inhibitors.
Antiviral Res. 160 17 24 (2018)
PMID: 30315877 DOI: 10.1016/j.antiviral.2018.10.006

Abstact

Zika virus NS2B-NS3 protease plays an essential role in viral replication by processing the viral polyprotein into individual proteins. The viral protease is therefore considered as an ideal antiviral drug target. To facilitate the development of protease inhibitors, we report three high-resolution co-crystal structures of bZiPro with peptidomimetic inhibitors composed of a P1-P4 segment and different P1' residues. Compounds 1 and 2 possess small P1' groups that are split off by bZiPro, which could be detected by mass spectrometry. On the other hand, the more potent compound 3 contains a bulky P1' benzylamide structure that is resistant to cleavage by bZiPro, demonstrating that presence of an uncleavable C-terminal cap contributes to a slightly improved inhibitory potency. The N-terminal phenylacetyl residue occupies a position above the P1 side chain and therefore stabilizes a horseshoe-like backbone conformation of the bound inhibitors. The P4 moieties show unique intra- and intermolecular interactions. Our work reports the detailed binding mode interactions of substrate-analogue inhibitors within the S4-S1' pockets and explains the preference of bZiPro for basic P1-P3 residues. These new structures of protease-inhibitor complexes will guide the design of more effective NS2B-NS3 protease inhibitors with improved potency and bioavailability.

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Primary Citation of related structures