9GZV | pdb_00009gzv

Crystal structure of human NUDT14 in complex with a potent inhibitor

PDB DOI: https://doi.org/10.2210/pdb9GZV/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-04 Released: 2025-10-15
Deposition Author(s): Balikci, E., Feyerherm, C., Bradshaw, W., Apostolidou, M., Adcock, C., McGown, A., Spencer, J., Huber, K.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.235 (Depositor), 0.235 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human NUDT14 in complex with an inhibitor (MA-955-9)

Balikci, E., Feyerherm, C., Bradshaw, W., Apostolidou, M., Adcock, C., McGown, A., Spencer, J., Huber, K.

To be published.

Macromolecule Content

Total Structure Weight: 50.45 kDa
Atom Count: 3,656
Modeled Residue Count: 437
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine diphosphate glucose pyrophosphatase NUDT14	A, B	223	Homo sapiens	Mutation(s): 0 Gene Names: NUDT14, UGPP EC: 3.6.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for O95848 (Homo sapiens) Explore O95848 Go to UniProtKB: O95848
PHAROS: O95848 GTEx: ENSG00000183828
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95848
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IRF Query on A1IRF Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain C [auth A]	C [auth A], H [auth A], L [auth B]	1-(1-methylpiperidin-4-yl)-3-(3-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-4-amine C₂₃ H₂₄ N₆ O JWZBPGIFSZRCBO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth A] Focus chain L [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], O [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A]	E [auth A], N [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]