5ZFI

Mouse kallikrein 7 in complex with 6-benzyl-1,4-diazepan-7-one derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based drug design to overcome species differences in kallikrein 7 inhibition of 1,3,6-trisubstituted 1,4-diazepan-7-ones.

Murafuji, H.Sugawara, H.Goto, M.Oyama, Y.Sakai, H.Imajo, S.Tomoo, T.Muto, T.

(2018) Bioorg. Med. Chem. 26: 3639-3653

  • DOI: 10.1016/j.bmc.2018.05.044
  • Primary Citation of Related Structures:  
  • Also Cited By: 6AHS

  • PubMed Abstract: 
  • A series of 1,3,6-trisubstituted 1,4-diazepan-7-ones were prepared as kallikrein 7 (KLK7, stratum corneum chymotryptic enzyme) inhibitors. Previously reported compounds 1-3 were potent human KLK7 inhibitors; however, they did not exhibit inhibitory a ...

    A series of 1,3,6-trisubstituted 1,4-diazepan-7-ones were prepared as kallikrein 7 (KLK7, stratum corneum chymotryptic enzyme) inhibitors. Previously reported compounds 1-3 were potent human KLK7 inhibitors; however, they did not exhibit inhibitory activity against mouse KLK7. Comparison of the human and mouse KLK7 structures reveals the cause of this species differences; therefore, compounds that could inhibit both KLK7s were designed, synthesized, and evaluated. Through this structure-based drug design, compound 22g was identified as an inhibitor against human and mouse KLK7, and only one of the enantiomers, (-)-22g, exhibited potent inhibitory activity. Furthermore, the crystal structure of mouse KLK7 complexed with 22g enabled the elucidation of structure-activity relationships and justified 22g as a valuable compound to overcome the species differences.


    Related Citations: 
    • Discovery and structure-activity relationship study of 1,3,6-trisubstituted 1,4-diazepane-7-ones as novel human kallikrein 7 inhibitors.
      Murafuji, H.,Sakai, H.,Goto, M.,Imajo, S.,Sugawara, H.,Muto, T.
      (2017) Bioorg. Med. Chem. Lett. 27: 5272


    Organizational Affiliation

    Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: murafuji.hidenobu.bj@daiichisankyo.co.jp.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: muto.tsuyoshi.zu@daiichisankyo.co.jp.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kallikrein-7
A
224Mus musculusMutation(s): 0 
Gene Names: Klk7 (Prss6, Scce)
EC: 3.4.21.117
Find proteins for Q91VE3 (Mus musculus)
Go to UniProtKB:  Q91VE3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9C9
Query on 9C9

Download SDF File 
Download CCD File 
A
2-[(3Z,6R)-6-[(2,6-dichlorophenyl)methyl]-3-(dimethylhydrazinylidene)-7-oxo-1,4-diazepan-1-yl]-N-[3-(1-methyl-1H-pyrazol-4-yl)phenyl]acetamide
C26 H29 Cl2 N7 O2
GKZIYEBJQVXMQL-GOSISDBHSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9C9IC50: 1200 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.850α = 90.00
b = 70.850β = 90.00
c = 98.022γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-03-06 
  • Released Date: 2018-06-27 
  • Deposition Author(s): Sugawara, H.

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-04
    Type: Data collection, Database references