3VFE | pdb_00003vfe

Virtual Screening and X-Ray Crystallography for Human Kallikrein 6 Inhibitors with an Amidinothiophene P1 Group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0HLClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Virtual Screening and X-ray Crystallography for Human Kallikrein 6 Inhibitors with an Amidinothiophene P1 Group.

Liang, G.Chen, X.Aldous, S.Pu, S.F.Mehdi, S.Powers, E.Giovanni, A.Kongsamut, S.Xia, T.Zhang, Y.Wang, R.Gao, Z.Merriman, G.McLean, L.R.Morize, I.

(2012) ACS Med Chem Lett 3: 159-164

  • DOI: https://doi.org/10.1021/ml200291e
  • Primary Citation of Related Structures:  
    3VFE

  • PubMed Abstract: 

    A series of compounds with an amidinothiophene P1 group and a pyrrolidinone-sulphonamide scaffold linker was identified as potent inhibitors of human kallikrein 6 by structure-based virtual screening based on the union accessible binding space of serine proteases. As the first series of potent nonmechanism-based hK6 inhibitors, they may be used as tool compounds for target validation. An X-ray structure of a representative compound complexed with hK6, resolved at a resolution of 1.88 Å, revealed that the amidinothiophene moiety bound in the S1 pocket and the pyrrolidinone-sulphonamide linker projected the aromatic tail into the S' pocket.


  • Organizational Affiliation

    Molecular Innovative Therapeutics, Fibrosis and Wound Repair, Global Pharmacovigilance & Epidemiology, Immunology and Inflammation Unit, Early to Candidate Unit, Aging Therapeutic Unit, and Biologics, Sanofi Pharmaceuticals , 1041 Route 202/206, Mailstop 203A, Bridgewater, New Jersey 08807, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kallikrein-6223Homo sapiensMutation(s): 3 
Gene Names: KLK6PRSS18PRSS9
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q92876 (Homo sapiens)
Explore Q92876 
Go to UniProtKB:  Q92876
PHAROS:  Q92876
GTEx:  ENSG00000167755 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92876
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0HL
Query on 0HL

Download Ideal Coordinates CCD File 
B [auth A]4-{[(3R)-3-{[(7-methoxynaphthalen-2-yl)sulfonyl](thiophen-3-ylmethyl)amino}-2-oxopyrrolidin-1-yl]methyl}thiophene-2-carboximidamide
C26 H26 N4 O4 S3
GWOFKCKOEZWDOK-HSZRJFAPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.938α = 90
b = 47.909β = 90
c = 107.553γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0HLClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-05-01
    Changes: Database references
  • Version 1.4: 2024-11-06
    Changes: Structure summary