9ECG | pdb_00009ecg

PANK3 complex structure with compound PZ-5588


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.237 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of Sulfonamide Pantothenate Kinase Activators and Elucidation of the Role of Isoform Selectivity in Cellular Pantothenate Kinase Activation.

Coker, A.L.Tangallapally, R.Yun, M.K.Subramanian, C.Jayasinghe, T.Miller, K.Edwards, A.Frank, M.Jackowski, S.Rock, C.O.White, S.W.Lee, R.E.

(2026) J Med Chem 69: 6004-6013

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c03452
  • Primary Citation Related Structures: 
    7UER, 7UES, 7UEU, 7UEV, 7UEY, 9D2O, 9D2P, 9ECG, 9ECH

  • PubMed Abstract: 

    Coenzyme A (CoA) biosynthesis is controlled by the four isoforms of the rate-limiting enzyme pantothenate kinase (PANK), whose tissue expression and subcellular localization regulate CoA homeostasis. Pantazines are positive allosteric modulators of PANK that increase cellular CoA levels by disrupting feedback inhibition by acyl-CoA esters. In this study, a structure-guided design was used to modify the Pantazine scaffold near the ATP-binding site to address metabolic liabilities of earlier leads. Replacement of a metabolically labile cyclopropyl group with a sulfonamide introduced a new hydrogen-bonding interaction with the γ-phosphate of ATP in the PANK3•ATP•Pantazine complex. This interaction improved ligand affinity, solubility, and metabolic stability. Analysis of isoform-specific inhibition revealed that cellular CoA elevation correlates with the difference in affinity between PANK3 and PANK1β, defining an "activation window" for CoA induction. Lead sulfonamide Pantazines were metabolically stable and increased hepatic CoA levels, supporting their potential for treating metabolic CoA deficiencies.


  • Organizational Affiliation
    • Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas PI, Memphis, Tennessee 38105, United States.

Macromolecule Content 

  • Total Structure Weight: 43.26 kDa 
  • Atom Count: 2,885 
  • Modeled Residue Count: 352 
  • Deposited Residue Count: 380 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pantothenate kinase 3380Homo sapiensMutation(s): 0 
Gene Names: PANK3
EC: 2.7.1.33
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H999 (Homo sapiens)
Explore Q9H999 
Go to UniProtKB:  Q9H999
PHAROS:  Q9H999
GTEx:  ENSG00000120137 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H999
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP

Query on ANP



Download:Ideal Coordinates CCD File
E [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
A1BHG
(Subject of Investigation/LOI)

Query on A1BHG



Download:Ideal Coordinates CCD File
D [auth A]N-(4-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}-2-fluorophenyl)ethanesulfonamide
C18 H21 Cl F N5 O3 S
HPXFKNAPMISREJ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.237 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.431α = 90
b = 98.431β = 90
c = 68.795γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata processing
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references