2YOL

West Nile Virus NS2B-NS3 protease in complex with 3,4- dichlorophenylacetyl-Lys-Lys-GCMA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Development and Characterization of New Peptidomimetic Inhibitors of the West Nile Virus Ns2B-Ns3 Protease.

Hammamy, M.Z.Haase, C.Hammami, M.Hilgenfeld, R.Steinmetzer, T.

(2013) ChemMedChem 8: 231

  • DOI: 10.1002/cmdc.201200497
  • Primary Citation of Related Structures:  
    2YOL

  • PubMed Abstract: 
  • A series of new substrate analogue inhibitors of the WNV NS2B-NS3 protease containing decarboxylated arginine mimetics at the P1 position was developed. Among the various analogues, trans-(4-guanidino)cyclohexylmethylamide (GCMA) was identified as the most suitable P1 residue ...

    A series of new substrate analogue inhibitors of the WNV NS2B-NS3 protease containing decarboxylated arginine mimetics at the P1 position was developed. Among the various analogues, trans-(4-guanidino)cyclohexylmethylamide (GCMA) was identified as the most suitable P1 residue. In combination with dichloro-substituted phenylacetyl groups at the P4 position, three inhibitors with inhibition constants of <0.2 μM were obtained. These GCMA inhibitors have a better selectivity profile than the previously described agmatine analogues, and possess negligible affinity for the trypsin-like serine proteases thrombin, factor Xa, and matriptase. A crystal structure in complex with the WNV protease was determined for one of the most potent inhibitors, 3,4-dichlorophenylacetyl-Lys-Lys-GCMA (K(i)=0.13 μM). The inhibitor adopts a horseshoe-like conformation, most likely due to a hydrophobic contact between the P4 phenyl ring and the P1 cyclohexyl group, which is further stabilized by an intramolecular hydrogen bond between the P1 guanidino group and the P4 carbonyl oxygen atom. These inhibitors are stable, readily accessible, and have a noncovalent binding mode. Therefore, they may serve as suitable lead structures for further development.


    Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3A230West Nile virusMutation(s): 0 
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P06935 (West Nile virus)
Explore P06935 
Go to UniProtKB:  P06935
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EBN (Subject of Investigation/LOI)
Query on EBN

Download Ideal Coordinates CCD File 
C [auth A](S)-6-amino-N-((S)-6-amino-1-(((1r,4S)-4-guanidinocyclohexyl)methylamino)-1-oxohexan-2-yl)-2-(2-(3,4-dichlorophenyl)acetamido)hexanamide
C28 H46 Cl2 N8 O3
OWKCLMWSCHVRNJ-BTDFZRAWSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
D [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EBN PDBBind:  2YOL Ki: 130 (nM) from 1 assay(s)
BindingDB:  2YOL Ki: 130 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.7α = 90
b = 118.7β = 90
c = 66.3γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release