5FBQ

PI4KB in complex with Rab11 and the MI358 Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

PI4KB in complex with Rab11 and the MI358 Inhibitor

Chalupska, D., Mejdrova, I., Nencka, R., Boura, E.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta572Homo sapiensMutation(s): 0 
Gene Names: PI4KB, PIK4CB
EC: 2.7.1.67
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBF8 (Homo sapiens)
Explore Q9UBF8 
Go to UniProtKB:  Q9UBF8
PHAROS:  Q9UBF8
GTEx:  ENSG00000143393 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBF8
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-11A221Homo sapiensMutation(s): 0 
Gene Names: RAB11A, RAB11
UniProt & NIH Common Fund Data Resources
Find proteins for P62491 (Homo sapiens)
Explore P62491 
Go to UniProtKB:  P62491
PHAROS:  P62491
GTEx:  ENSG00000103769 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62491
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5W6
Query on 5W6
Download Ideal Coordinates CCD File 
C [auth A]~{N}-[2-[[6-chloranyl-3-[3-[4-(hydroxymethyl)piperidin-1-yl]sulfonyl-4-methoxy-phenyl]-2-methyl-imidazo[1,2-b]pyridazin-8-yl]amino]ethyl]ethanamide
C24 H31 Cl N6 O5 S
IEPPNMCWFCTFFK-UHFFFAOYSA-N
GDP
Query on GDP
Download Ideal Coordinates CCD File 
D [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5W6 BindingDB:  5FBQ IC50: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.759α = 90
b = 101.155β = 90
c = 188.486γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASESphasing

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: 2016-12-28
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description