9HBM | pdb_00009hbm

Crystal structure of human NUDT14 in complex with a potent inhibitor (MA-955-10)

• PDB DOI: https://doi.org/10.2210/pdb9HBM/pdb

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


• Deposited: 2024-11-07 Released: 2025-11-19 
• Deposition Author(s): Balikci, E., Feyerherm, C., Apostolidou, M., Adcock, C., McGown, A., Spencer, J., Huber, K.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.269 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human NUDT14 in complex with a potent inhibitor (MA-955-10)

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.24 kDa 
• Atom Count: 3,605 
• Modeled Residue Count: 439 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ITN (Subject of Investigation/LOI)	C [auth A], E [auth B]	1-(1-methylpiperidin-4-yl)-3-(4-propan-2-yloxyphenyl)pyrazolo[3,4-d]pyrimidin-4-amine C20 H26 N6 O VEHOUOASHQBMIK-UHFFFAOYSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.269 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.42	α = 90
b = 71.15	β = 90
c = 111.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Balikci, E., Feyerherm, C., Apostolidou, M., Adcock, C., McGown, A., Spencer, J., Huber, K.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	875510

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release