8QFW | pdb_00008qfw

Murine pyridoxal phosphatase in complex with 7,8-dihydroxyflavone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.209 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8QFW

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

7,8-Dihydroxyflavone is a direct inhibitor of human and murine pyridoxal phosphatase.

Brenner, M.Zink, C.Witzinger, L.Keller, A.Hadamek, K.Bothe, S.Neuenschwander, M.Villmann, C.von Kries, J.P.Schindelin, H.Jeanclos, E.Gohla, A.

(2024) Elife 13

  • DOI: https://doi.org/10.7554/eLife.93094
  • Primary Citation Related Structures: 
    8QFW, 8S8A, 9EM1

  • PubMed Abstract: 

    Vitamin B6 deficiency has been linked to cognitive impairment in human brain disorders for decades. Still, the molecular mechanisms linking vitamin B6 to these pathologies remain poorly understood, and whether vitamin B6 supplementation improves cognition is unclear as well. Pyridoxal 5'-phosphate phosphatase (PDXP), an enzyme that controls levels of pyridoxal 5'-phosphate (PLP), the co-enzymatically active form of vitamin B6, may represent an alternative therapeutic entry point into vitamin B6-associated pathologies. However, pharmacological PDXP inhibitors to test this concept are lacking. We now identify a PDXP and age-dependent decline of PLP levels in the murine hippocampus that provides a rationale for the development of PDXP inhibitors. Using a combination of small-molecule screening, protein crystallography, and biolayer interferometry, we discover, visualize, and analyze 7,8-dihydroxyflavone (7,8-DHF) as a direct and potent PDXP inhibitor. 7,8-DHF binds and reversibly inhibits PDXP with low micromolar affinity and sub-micromolar potency. In mouse hippocampal neurons, 7,8-DHF increases PLP in a PDXP-dependent manner. These findings validate PDXP as a druggable target. Of note, 7,8-DHF is a well-studied molecule in brain disorder models, although its mechanism of action is actively debated. Our discovery of 7,8-DHF as a PDXP inhibitor offers novel mechanistic insights into the controversy surrounding 7,8-DHF-mediated effects in the brain.


  • Organizational Affiliation
    • Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 64.26 kDa 
  • Atom Count: 4,920 
  • Modeled Residue Count: 578 
  • Deposited Residue Count: 586 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chronophin
A, B
293Mus musculusMutation(s): 0 
Gene Names: PdxpCinPlpPlpp
EC: 3.1.3.16 (PDB Primary Data), 3.1.3.74 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P60487 (Mus musculus)
Explore P60487 
Go to UniProtKB:  P60487
IMPC:  MGI:1919282
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60487
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UK9
(Subject of Investigation/LOI)

Query on UK9



Download:Ideal Coordinates CCD File
E [auth A]7,8-bis(oxidanyl)-2-phenyl-chromen-4-one
C15 H10 O4
COCYGNDCWFKTMF-UHFFFAOYSA-N
CIT

Query on CIT



Download:Ideal Coordinates CCD File
G [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
F [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4
(Subject of Investigation/LOI)

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.209 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.011α = 90
b = 167.011β = 90
c = 167.011γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB688-A11

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references
  • Version 1.2: 2024-06-26
    Changes: Structure summary
  • Version 1.3: 2024-10-16
    Changes: Structure summary