4D8N

Human Kallikrein 6 Inhibitors with a para-Amidobenzylanmine P1 Group Carry a High Binding Efficiency


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Human kallikrein 6 inhibitors with a para-amidobenzylanmine P1 group identified through virtual screening.

Liang, G.Chen, X.Aldous, S.Pu, S.F.Mehdi, S.Powers, E.Xia, T.Wang, R.

(2012) Bioorg.Med.Chem.Lett. 22: 2450-2455

  • DOI: 10.1016/j.bmcl.2012.02.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A series of hK6 inhibitors with a para-amidobenzylamine P1 group and a 2-hydroxybenzamide scaffold linker was discovered through virtual screening. The X-ray structure of hK6 complexed with compound 9b was determined to a resolution of 1.68Å. The ter ...

    A series of hK6 inhibitors with a para-amidobenzylamine P1 group and a 2-hydroxybenzamide scaffold linker was discovered through virtual screening. The X-ray structure of hK6 complexed with compound 9b was determined to a resolution of 1.68Å. The tertiary folding of the hK6 complexed with the inhibitor is conserved relative to the structure of the apo-protein, whereas the interaction between hK6 and the inhibitor is consistent with both the SAR and the in silico model used in the virtual screening.


    Organizational Affiliation

    Molecular Innovative Therapeutics, Sanofi Pharmaceuticals, Bridgewater, NJ, USA. guyan.liang@verizon.net




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kallikrein-6
A
223Homo sapiensMutation(s): 3 
Gene Names: KLK6 (PRSS18, PRSS9)
EC: 3.4.21.-
Find proteins for Q92876 (Homo sapiens)
Go to Gene View: KLK6
Go to UniProtKB:  Q92876
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0HM
Query on 0HM

Download SDF File 
Download CCD File 
A
2-{[4-(aminomethyl)phenyl]carbamoyl}-1-[(1-benzyl-1H-imidazol-2-yl)methyl]-3-hydroxypyridinium
C24 H24 N5 O2
DMRCMJXUFJLJKH-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0HMIC50: 1800 nM BINDINGMOAD
0HMIC50: 1800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.185α = 90.00
b = 45.950β = 90.00
c = 109.077γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
CNXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSrefinement
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-04
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description