5YJP

Human chymase in complex with 3-(ethoxyimino)-7-oxo-1,4-diazepane derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based design, synthesis, and binding mode analysis of novel and potent chymase inhibitors

Futamura-Takahashi, J.Tanaka, T.Sugawara, H.Iwashita, S.Imajo, S.Oyama, Y.Muto, T.

(2018) Bioorg. Med. Chem. Lett. 28: 188-192

  • DOI: 10.1016/j.bmcl.2017.11.031
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Based on insight from the X-ray crystal structure of human chymase in complex with compound 1, a lactam carbonyl of the diazepane core was exchanged with O-substituted oxyimino group, leading to amidoxime derivatives. This modification resulted in hi ...

    Based on insight from the X-ray crystal structure of human chymase in complex with compound 1, a lactam carbonyl of the diazepane core was exchanged with O-substituted oxyimino group, leading to amidoxime derivatives. This modification resulted in highly potent chymase inhibitors, such as O-phenylamidoxime 5f. X-ray crystal structure analysis indicated that compound 5f induced movement of the Leu99 and Tyr94 side chains at the S2 site, and the increase in inhibitory activity of O-phenyl amidoxime derivatives suggested that the O-phenyl moiety interacted with the Tyr94 residue. Surface plasmon resonance experiments showed that compound 5f had slower association and dissociation kinetics and the calculated residence time of compound 5f to human chymase was extended compared to that of amide compound 1.


    Organizational Affiliation

    Asubio Pharma Co., Ltd, 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan. Electronic address: futamura.junko.b6@asubio.co.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
human chymase
A
226Homo sapiensMutation(s): 0 
Gene Names: CMA1 (CYH, CYM)
EC: 3.4.21.39
Find proteins for P23946 (Homo sapiens)
Go to Gene View: CMA1
Go to UniProtKB:  P23946
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
8W6
Query on 8W6

Download SDF File 
Download CCD File 
A
4-((R)-1-((R,Z)-6-(5-chloro-2-methoxybenzyl)-3-(ethoxyimino)-7-oxo-1,4-diazepane-1-carboxamido)propyl)benzoic acid
4-[(1R)-1-[[(3Z,6R)-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-3-ethoxyimino-7-oxidanylidene-1,4-diazepan-1-yl]carbonylamino]propyl]benzoic acid
C26 H31 Cl N4 O6
ZHZSQRPEOXQFJC-TZIWHRDSSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.155 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 75.089α = 90.00
b = 75.089β = 90.00
c = 49.750γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-10-11 
  • Released Date: 2017-12-27 
  • Deposition Author(s): Sugawara, H.

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Database references