4EN4

Crystal Structure of the Ternary Human PL Kinase-Ginkgotoxin-MgATP Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of human pyridoxal kinase in complex with the neurotoxins, ginkgotoxin and theophylline: insights into pyridoxal kinase inhibition.

Gandhi, A.K.Desai, J.V.Ghatge, M.S.di Salvo, M.L.Di Biase, S.Danso-Danquah, R.Musayev, F.N.Contestabile, R.Schirch, V.Safo, M.K.

(2012) PLoS One 7: e40954-e40954

  • DOI: 10.1371/journal.pone.0040954
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Several drugs and natural compounds are known to be highly neurotoxic, triggering epileptic convulsions or seizures, and causing headaches, agitations, as well as other neuronal symptoms. The neurotoxic effects of some of these compounds, including t ...

    Several drugs and natural compounds are known to be highly neurotoxic, triggering epileptic convulsions or seizures, and causing headaches, agitations, as well as other neuronal symptoms. The neurotoxic effects of some of these compounds, including theophylline and ginkgotoxin, have been traced to their inhibitory activity against human pyridoxal kinase (hPL kinase), resulting in deficiency of the active cofactor form of vitamin B₆, pyridoxal 5'-phosphate (PLP). Pyridoxal (PL), an inactive form of vitamin B₆ is converted to PLP by PL kinase. PLP is the B₆ vitamer required as a cofactor for over 160 enzymatic activities essential in primary and secondary metabolism. We have performed structural and kinetic studies on hPL kinase with several potential inhibitors, including ginkgotoxin and theophylline. The structural studies show ginkgotoxin and theophylline bound at the substrate site, and are involved in similar protein interactions as the natural substrate, PL. Interestingly, the phosphorylated product of ginkgotoxin is also observed bound at the active site. This work provides insights into the molecular basis of hPL kinase inhibition and may provide a working hypothesis to quickly screen or identify neurotoxic drugs as potential hPL kinase inhibitors. Such adverse effects may be prevented by administration of an appropriate form of vitamin B₆, or provide clues of how to modify these drugs to help reduce their hPL kinase inhibitory effects.


    Organizational Affiliation

    Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxal kinaseA, B312Homo sapiensMutation(s): 0 
Gene Names: PDXKC21orf124C21orf97PKHPNKPRED79
EC: 2.7.1.35
Find proteins for O00764 (Homo sapiens)
Explore O00764 
Go to UniProtKB:  O00764
NIH Common Fund Data Resources
PHAROS  O00764
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
GT1
Query on GT1

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A, B
[5-hydroxy-4-(methoxymethyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate
C9 H14 N O6 P
RFYDYCIMPLKICN-UHFFFAOYSA-N
 Ligand Interaction
GT0
Query on GT0

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A, B
5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol
C9 H13 N O3
SVINQHQHARVZFF-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GT0Ki :  3000   nM  PDBBind
GT0Ki:  3000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.219 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.749α = 90
b = 115.221β = 90
c = 169.554γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Database references