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), 0.222 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 24.97 kDa 
  • Atom Count: 1,896 
  • Modeled Residue Count: 222 
  • Deposited Residue Count: 223 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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), 0.222 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.194 (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 


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