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 

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Ligand Structure Quality Assessment 


This is version 1.0 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Segment polarity protein dishevelled homolog DVL-1A102Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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