6LCB

Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009

Yasukochi, S.Numoto, N.Tenno, N.Tenno, T.Ito, N.Hiroaki, H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Segment polarity protein dishevelled homolog DVL-1102Homo sapiensMutation(s): 2 
Gene Names: DVL1
UniProt & NIH Common Fund Data Resources
Find proteins for O14640 (Homo sapiens)
Explore O14640 
Go to UniProtKB:  O14640
PHAROS:  O14640
GTEx:  ENSG00000107404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14640
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E83 (Subject of Investigation/LOI)
Query on E83

Download Ideal Coordinates CCD File 
B [auth A]2-[[3-[(2E)-2-[1,3-bis(oxidanylidene)-1-phenyl-butan-2-ylidene]hydrazinyl]phenyl]sulfonylamino]benzoic acid
C23 H19 N3 O6 S
SOWABNTWBBBOPH-NJNXFGOHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.375α = 90
b = 85.375β = 90
c = 46.167γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description