9GEM | pdb_00009gem

Crystal structure of human NUDT14 in complex with MA-12

PDB DOI: https://doi.org/10.2210/pdb9GEM/pdb

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

Deposited: 2024-08-07 Released: 2026-02-18
Deposition Author(s): Koekemoer, L., Dlamini, L.S., Gurav, N., Apostolidou, M., Adcock, C., McGown, A., Spencer, J., Huber, K.V.M.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.287 (Depositor), 0.287 (DCC)
R-Value Work:
0.215 (Depositor), 0.215 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of human NUDT14 in complex with MA-12

Koekemoer, L., Gurav, N., Apostolidou, M., Adcock, C., McGown, A., Spencer, J., Huber, K.V.M.

To be published.

Macromolecule Content

Total Structure Weight: 97.71 kDa
Atom Count: 6,379
Modeled Residue Count: 799
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine diphosphate glucose pyrophosphatase NUDT14	A, B, C, D	222	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IJI (Subject of Investigation/LOI) Query on A1IJI Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth D]	1-(1-methylpiperidin-4-yl)-3-[4-[(2-methylpropan-2-yl)oxy]phenyl]pyrazolo[3,4-d]pyrimidin-4-amine C₂₁ H₂₈ N₆ O QVHDSGJMUBFNQB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.287 (Depositor), 0.287 (DCC)
R-Value Work: 0.215 (Depositor), 0.215 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.919	α = 90
b = 107.191	β = 93.624
c = 78.114	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Apostolidou, M.

Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	875510

Revision History (Full details and data files)

Version 1.0: 2026-02-18
Type: Initial release
Version 1.1: 2026-05-13
Changes: Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.