9HI0 | pdb_00009hi0

STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH COMPOUND WBX04

PDB DOI: https://doi.org/10.2210/pdb9HI0/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-22 Released: 2025-12-03
Deposition Author(s): Mouilleron, S., Schumann, B., Browne, W., Purkiss, A., Weckwerth, T., Ogrodowicz, R., Prema, R., Kunzelmann, S., Roustan, C.
Funding Organization(s): Engineering and Physical Sciences Research Council, The Francis Crick Institute, Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free:
0.190 (Depositor), 0.192 (DCC)
R-Value Work:
0.154 (Depositor), 0.161 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Identification of Novel Inhibitors of Human UDP-Galactose-4-Epimerase (GalE) by Fragment-Based Lead Discovery

Browne, W., Schumann, B., Purkiss, A., Weckwerth, T., Ogrodowicz, R., Prema, R., Kunzelmann, S., Roustan, C., Mouilleron, S.

To be published.

Macromolecule Content

Total Structure Weight: 78.31 kDa
Atom Count: 6,052
Modeled Residue Count: 689
Deposited Residue Count: 690
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 4-epimerase	A [auth B], B [auth A]	345	Homo sapiens	Mutation(s): 0 Gene Names: GALE EC: 5.1.3.2 (PDB Primary Data), 5.1.3.7 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14376 (Homo sapiens) Explore Q14376 Go to UniProtKB: Q14376
PHAROS: Q14376 GTEx: ENSG00000117308
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14376
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain K [auth A] MOL2 format, chain E [auth B] MOL2 format, chain K [auth A] mmCIF format, chain E [auth B] mmCIF format, chain K [auth A]	E [auth B], K [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth B] Focus chain K [auth A] Interactions & Density Focus chain E [auth B] Focus chain K [auth A]
A1IU2 (Subject of Investigation/LOI) Query on A1IU2 Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain L [auth A] MOL2 format, chain F [auth B] MOL2 format, chain L [auth A] mmCIF format, chain F [auth B] mmCIF format, chain L [auth A]	F [auth B], L [auth A]	3-[(5-methyl-1,2-oxazol-3-yl)carbamoylamino]-~{N}-pyridin-4-yl-propanamide C₁₃ H₁₅ N₅ O₃ CHTQBKADVVXGAL-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain L [auth A] Interactions & Density Focus chain F [auth B] Focus chain L [auth A]
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	C [auth B], D [auth B], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free: 0.190 (Depositor), 0.192 (DCC)
R-Value Work: 0.154 (Depositor), 0.161 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.358	α = 90
b = 46.3	β = 90
c = 110.727	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/S023518/1
The Francis Crick Institute	United Kingdom	CC2127
The Francis Crick Institute	United Kingdom	CC2127
Wellcome Trust	United Kingdom	CC2127