6S8L

Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes

La Sala, G.Olieric, N.

(2019) Chem 


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain451Homo sapiensMutation(s): 0 
Gene Names: TUBA1B
UniProt & NIH Common Fund Data Resources
Find proteins for P68363 (Homo sapiens)
Explore P68363 
Go to UniProtKB:  P68363
GTEx:  ENSG00000123416 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68363
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-3 chain450Homo sapiensMutation(s): 0 
Gene Names: TUBB3TUBB4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13509 (Homo sapiens)
Explore Q13509 
Go to UniProtKB:  Q13509
GTEx:  ENSG00000258947 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13509
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Designed ankyrin repeat protein (DARPIN) D1C [auth F]157synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PN6 BindingDB:  6S8L Kd: min: 1000, max: 1060 (nM) from 2 assay(s)
IC50: 1800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.63α = 90
b = 91.2β = 97.49
c = 82.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata 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: 2019-11-27
    Type: Initial release