5YJM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    5YJP, 5YJM

  • 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 highly potent chymase inhibitors, such as O-phenylamidoxime 5f ...

    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: muto.tsuyoshi.ba@asubio.co.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
human chymase A226Homo sapiensMutation(s): 0 
Gene Names: CMA1CYHCYM
EC: 3.4.21.39
Find proteins for P23946 (Homo sapiens)
Explore P23946 
Go to UniProtKB:  P23946
NIH Common Fund Data Resources
PHAROS:  P23946
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8W3
Query on 8W3

Download Ideal Coordinates CCD File 
A
2-amino-4-((R)-1-((R,Z)-6-(5-chloro-2-methoxybenzyl)-7-oxo-3-(phenoxyimino)-1,4-diazepane-1-carboxamido)propyl)benzoic acid
C30 H32 Cl N5 O6
LHASZEBEQGPCFM-CJFMBICVSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8W3IC50:  8.899999618530273   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.089α = 90
b = 75.089β = 90
c = 49.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary