7RCM | pdb_00007rcm

Crystal Structure of ADP-bound Galactokinase

  • Classification: SUGAR BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2021-07-07 Released: 2021-09-29 
  • Deposition Author(s): Whitby, F.G.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view detailsBest fitted GLAClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Structure-Based Optimization of Small Molecule Human Galactokinase Inhibitors.

Liu, L.Tang, M.Pragani, R.Whitby, F.G.Zhang, Y.Q.Balakrishnan, B.Fang, Y.Karavadhi, S.Tao, D.LeClair, C.A.Hall, M.D.Marugan, J.J.Boxer, M.Shen, M.Hill, C.P.Lai, K.Patnaik, S.

(2021) J Med Chem 64: 13551-13571

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00945
  • Primary Citation of Related Structures:  
    7RCL, 7RCM, 7S49, 7S4C

  • PubMed Abstract: 

    Classic galactosemia is a rare disease caused by inherited deficiency of galactose-1 phosphate uridylyltransferase (GALT). Accumulation of galactose-1 phosphate (gal-1P) is thought to be the major cause of the chronic complications associated with this disease, which currently has no treatment. Inhibiting galactokinase (GALK1), the enzyme that generates galactose-1 phosphate, has been proposed as a novel strategy for treating classic galactosemia. Our previous work identified a highly selective unique dihydropyrimidine inhibitor against GALK1. With the determination of a co-crystal structure of this inhibitor with human GALK1, we initiated a structure-based structure-activity relationship (SAR) optimization campaign that yielded novel analogs with potent biochemical inhibition (IC 50 < 100 nM). Lead compounds were also able to prevent gal-1P accumulation in patient-derived cells at low micromolar concentrations and have pharmacokinetic properties suitable for evaluation in rodent models of galactosemia.


  • Organizational Affiliation

    National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galactokinase
A, B
392Homo sapiensMutation(s): 2 
Gene Names: GALK1GALK
EC: 2.7.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P51570 (Homo sapiens)
Explore P51570 
Go to UniProtKB:  P51570
PHAROS:  P51570
GTEx:  ENSG00000108479 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51570
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
GLA
Query on GLA

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
L [auth B]
M [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
P [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
Q [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.793α = 90
b = 128.793β = 90
c = 240.652γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view detailsBest fitted GLAClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2021-09-29 
  • Deposition Author(s): Whitby, F.G.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1HD074844

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary