8PTT | pdb_00008ptt

Human NUDT5 in complex with MRK-952

PDB DOI: https://doi.org/10.2210/pdb8PTT/pdb

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

Deposited: 2023-07-14 Released: 2024-07-24
Deposition Author(s): Diaz-Saez, L., Koekemoer, L., Feyerherm, C., Sloman, S., Fischer, C., Schneider, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Huber, K.V.M.
Funding Organization(s): The Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.245 (Depositor), 0.245 (DCC)
R-Value Work:
0.178 (Depositor), 0.183 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Human NUDT5 in complex with MRK-952

Diaz-Saez, L., Koekemoer, L., Feyerherm, C., Sloman, S., Fischer, C., Schneider, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Huber, K.V.M.

To be published.

Macromolecule Content

Total Structure Weight: 99.34 kDa
Atom Count: 6,589
Modeled Residue Count: 783
Deposited Residue Count: 876
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-sugar pyrophosphatase	A, B, C, D	219	Homo sapiens	Mutation(s): 0 Gene Names: NUDT5, NUDIX5, HSPC115 EC: 3.6.1.13 (PDB Primary Data), 3.6.1.58 (PDB Primary Data), 2.7.7.96 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKK9 (Homo sapiens) Explore Q9UKK9 Go to UniProtKB: Q9UKK9
PHAROS: Q9UKK9 GTEx: ENSG00000165609
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UKK9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F2V (Subject of Investigation/LOI) Query on F2V Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], K [auth C], N [auth D]	6-[(5~{R})-7-[3-chloranyl-4-(trifluoromethyl)phenyl]-2,7-diazaspiro[4.4]nonan-2-yl]-7-methyl-purine C₂₀ H₂₀ Cl F₃ N₆ CAPZLSKZPWSIKV-LJQANCHMSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain N [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A] H [auth B] I [auth B] J [auth B] L [auth C] F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D]