9FL6 | pdb_00009fl6

Human NUDT1 with medetomidine

PDB DOI: https://doi.org/10.2210/pdb9FL6/pdb

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

Deposited: 2024-06-04 Released: 2025-06-18
Deposition Author(s): Salah, E., Huber, K.V.M., Elkins, J.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.159 (Depositor), 0.167 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

NUDT1 with medetomidine

Salah, E., Huber, K.V.M., Elkins, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 18.36 kDa
Atom Count: 1,467
Modeled Residue Count: 154
Deposited Residue Count: 158
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform p26 of Oxidized purine nucleoside triphosphate hydrolase	A [auth AAA]	158	Homo sapiens	Mutation(s): 0 Gene Names: NUDT1, MTH1 EC: 3.6.1.56 (PDB Primary Data), 3.6.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P36639 (Homo sapiens) Explore P36639 Go to UniProtKB: P36639
PHAROS: P36639 GTEx: ENSG00000106268
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36639
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IFR (Subject of Investigation/LOI) Query on A1IFR Download:Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	5-[(1~{R})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole C₁₃ H₁₆ N₂ CUHVIMMYOGQXCV-LLVKDONJSA-N		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.159 (Depositor), 0.167 (DCC)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.739	α = 90
b = 60.85	β = 90
c = 67.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	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: 2025-06-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-06-18
Type: Initial release

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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.