3N7O

X-ray structure of human chymase in complex with small molecule inhibitor.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chymase226Homo sapiensMutation(s): 2 
Gene Names: chymase (16-245), CMA1, CYH, CYM
EC: 3.4.21.39
UniProt & NIH Common Fund Data Resources
Find proteins for P23946 (Homo sapiens)
Explore P23946 
Go to UniProtKB:  P23946
PHAROS:  P23946
GTEx:  ENSG00000092009 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23946
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N7O
Query on N7O
Download Ideal Coordinates CCD File 
D [auth A](S)-[(1S)-1-(5-chloro-1-benzothiophen-3-yl)-2-{[(E)-2-(3,4-difluorophenyl)ethenyl]amino}-2-oxoethyl]methylphosphinic acid
C19 H15 Cl F2 N O3 P S
SEXLHAASDZPHOM-DKFQHHCZSA-N
UNL
Query on UNL
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]		Unknown ligand
SEXLHAASDZPHOM-DKFQHHCZSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
N7O PDBBind:  3N7O Ki: 72 (nM) from 1 assay(s)
Binding MOAD:  3N7O Ki: 72 (nM) from 1 assay(s)
BindingDB:  3N7O IC50: 58 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.475α = 90
b = 124.475β = 90
c = 124.475γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-06
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary