5Y9L

Human kallikrein 7 in complex with 1,3,6-trisubstituted 1,4-diazepane-7-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 5272-5276

  • DOI: 10.1016/j.bmcl.2017.10.030
  • Primary Citation of Related Structures:  
  • Also Cited By: 6AHS, 5ZFI, 5ZFH

  • PubMed Abstract: 
  • Compound 1, composed of a 1,3,6-trisubstituted 1,4-diazepane-7-one, was discovered as a novel human kallikrein 7 (KLK7, stratum corneum chymotryptic enzyme, SCCE) inhibitor, and its derivatives were synthesized and evaluated. Structure-activity relat ...

    Compound 1, composed of a 1,3,6-trisubstituted 1,4-diazepane-7-one, was discovered as a novel human kallikrein 7 (KLK7, stratum corneum chymotryptic enzyme, SCCE) inhibitor, and its derivatives were synthesized and evaluated. Structure-activity relationship studies of the amidoxime unit and benzoic acid part of this new scaffold led to the identification of 25 and 34, which were more potent than the hit compound, 1. The X-ray co-crystal structure of compound 25 and human KLK7 revealed the characteristic interactions and enabled explanations of the structure-activity relationship.


    Organizational Affiliation

    Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: murafuji.hidenobu.bc@asubio.co.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kallikrein-7
A
224Homo sapiensMutation(s): 0 
Gene Names: KLK7 (PRSS6, SCCE)
EC: 3.4.21.117
Find proteins for P49862 (Homo sapiens)
Go to Gene View: KLK7
Go to UniProtKB:  P49862
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8R3
Query on 8R3

Download SDF File 
Download CCD File 
A
3-[2-[(3Z,6R)-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-3-(dimethylhydrazinylidene)-7-oxidanylidene-1,4-diazepan-1-yl]ethanoylamino]benzoic acid
C24 H28 Cl N5 O5
STRUTOBZXDUGAL-QGZVFWFLSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.208 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.895α = 90.00
b = 90.926β = 90.00
c = 92.030γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-08-25 
  • Released Date: 2017-11-29 
  • Deposition Author(s): Sugawara, H.

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release