9H6P | pdb_00009h6p

Crystal structure of NUDT14 complexed with novel compound AMNUDT14-003 in spacegroup P1

• PDB DOI: https://doi.org/10.2210/pdb9H6P/pdb

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


• Deposited: 2024-10-24 Released: 2025-11-05 
• Deposition Author(s): Balikci, E., Koekemoer, L., Dlamini, L.S., Gurav, N., Apostolidou, M., Adcock, C., McGown, A., Marques, A.M.C., Spencer, J., Huber, K.V.M., Structural Genomics Consortium (SGC)
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 
  0.265 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.211 (DCC) 

Starting Model: experimental

Literature

Crystal structure of NUDT14 complexed with novel compound AMNUDT14-003 in spacegroup

Balikci, E., Koekemoer, L., Dlamini, L.S., Gurav, N., Apostolidou, M., Adcock, C., McGown, A., Marques, A.M.C., Spencer, J., Huber, K.V.M.

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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 194.52 kDa 
• Atom Count: 12,965 
• Modeled Residue Count: 1,672 
• Deposited Residue Count: 1,776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine diphosphate glucose pyrophosphatase NUDT14	A, B, C, D, E, F, G, H	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ISQ (Subject of Investigation/LOI)	I [auth A], J [auth C], K [auth D], L [auth H]	3-(1H-indol-6-yl)-1-(1-methylpiperidin-4-yl)pyrazolo[3,4-d]pyrimidin-4-amine C19 H21 N7 XWRZTNJWUCCXRZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free:  0.265 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.211 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.886	α = 89.955
b = 85.392	β = 89.998
c = 106.742	γ = 78.77

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Balikci, E., Koekemoer, L., Dlamini, L.S., Gurav, N., Apostolidou, M., Adcock, C., McGown, A., Marques, A.M.C., Spencer, J., Huber, K.V.M., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	875510

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release