7S49 | pdb_00007s49

Crystal Structure of Inhibitor-bound Galactokinase

PDB DOI: https://doi.org/10.2210/pdb7S49/pdb

Classification: Transferase/Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-09-08 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: 2.20 Å
R-Value Free:
0.226 (Depositor), 0.226 (DCC)
R-Value Work:
0.158 (Depositor), 0.158 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 34491744 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.1c00945
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 85.96 kDa
Atom Count: 6,267
Modeled Residue Count: 782
Deposited Residue Count: 784
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactokinase	A, B	392	Homo sapiens	Mutation(s): 2 Gene Names: GALK1, GALK 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51570
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4QI (Subject of Investigation/LOI) Query on 4QI Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B]	(4R)-2-[(1,3-benzoxazol-2-yl)amino]-4-(4-chloro-1H-pyrazol-5-yl)-4,6,7,8-tetrahydroquinazolin-5(1H)-one C₁₈ H₁₅ Cl N₆ O₂ ORBGGGFENULXFO-MRXNPFEDSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
GLA Query on GLA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], K [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]