7ZEH | pdb_00007zeh

Human cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7Guanine

PDB DOI: https://doi.org/10.2210/pdb7ZEH/pdb

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

Deposited: 2022-03-31 Released: 2022-05-25
Deposition Author(s): Kubacka, D., Kozarski, M., Baranowski, M.R., Wojcik, R., Jemielity, J., Kowalska, J., Basquin, J.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.220 (Depositor), 0.218 (DCC)
R-Value Work:
0.188 (Depositor), 0.185 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism.

Kubacka, D., Kozarski, M., Baranowski, M.R., Wojcik, R., Panecka-Hofman, J., Strzelecka, D., Basquin, J., Jemielity, J., Kowalska, J.

(2022) Pharmaceuticals (Basel) 15

PubMed: 35631380 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/ph15050554
Primary Citation Related Structures:
7ZEE, 7ZEG, 7ZEH

PubMed Abstract:
Cytosolic nucleotidases (cNs) catalyze dephosphorylation of nucleoside 5'-monophosphates and thereby contribute to the regulation of nucleotide levels in cells. cNs have also been shown to dephosphorylate several therapeutically relevant nucleotide analogues. cN-IIIB has shown in vitro a distinctive activity towards 7-mehtylguanosine monophosphate (m ⁷GMP), which is one key metabolites of mRNA cap. Consequently, it has been proposed that cN-IIIB participates in mRNA cap turnover and prevents undesired accumulation and salvage of m ⁷GMP. Here, we sought to develop molecular tools enabling more advanced studies on the cellular role of cN-IIIB. To that end, we performed substrate and inhibitor property profiling using a library of 41 substrate analogs. The most potent hit compounds (identified among m ⁷GMP analogs) were used as a starting point for structure-activity relationship studies. As a result, we identified several 7-benzylguanosine 5'-monophosphate (Bn ⁷GMP) derivatives as potent, unhydrolyzable cN-IIIB inhibitors. The mechanism of inhibition was elucidated using X-ray crystallography and molecular docking. Finally, we showed that compounds that potently inhibit recombinant cN-IIIB have the ability to inhibit m ⁷GMP decay in cell lysates.

Organizational Affiliation

Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.

Macromolecule Content

Total Structure Weight: 143.08 kDa
Atom Count: 10,071
Modeled Residue Count: 1,104
Deposited Residue Count: 1,208
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7-methylguanosine phosphate-specific 5'-nucleotidase	A, B, C, D	302	Homo sapiens	Mutation(s): 0 Gene Names: NT5C3B, NT5C3L EC: 3.1.3.91 (PDB Primary Data), 3.1.3.5 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q969T7 (Homo sapiens) Explore Q969T7 Go to UniProtKB: Q969T7
PHAROS: Q969T7 GTEx: ENSG00000141698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q969T7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPQ (Subject of Investigation/LOI) Query on IPQ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth B] SDF format, chain PA [auth D] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain Z [auth C]	E [auth A], P [auth B], PA [auth D], Z [auth C]	N7-(3,4-difluorobenzyl) guanine C₁₂ H₁₀ F₂ N₅ O NBTRICCNNMIXFE-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Z [auth C]
RBL (Subject of Investigation/LOI) Query on RBL Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain F [auth A] SDF format, chain Q [auth B] SDF format, chain QA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth D]	AA [auth C], F [auth A], Q [auth B], QA [auth D]	D-ribulose C₅ H₁₀ O₅ ZAQJHHRNXZUBTE-NQXXGFSBSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain Q [auth B] Focus chain QA [auth D] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain Q [auth B] Focus chain QA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain Y [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain Y [auth B]	AB [auth D], NA [auth C], O [auth A], Y [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth D] Focus chain NA [auth C] Focus chain O [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AB [auth D] Focus chain NA [auth C] Focus chain O [auth A] Focus chain Y [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain X [auth B] SDF format, chain ZA [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain X [auth B] mmCIF format, chain ZA [auth D]	MA [auth C], N [auth A], X [auth B], ZA [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain MA [auth C] Focus chain N [auth A] Focus chain X [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain MA [auth C] Focus chain N [auth A] Focus chain X [auth B] Focus chain ZA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain OA [auth D] SDF format, chain R [auth B] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] FA [auth C] BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], OA [auth D], R [auth B], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], VA [auth D], WA [auth D], XA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain OA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain OA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain W [auth B] SDF format, chain YA [auth D] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain W [auth B] MOL2 format, chain YA [auth D] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain W [auth B] mmCIF format, chain YA [auth D]	LA [auth C], M [auth A], W [auth B], YA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain LA [auth C] Focus chain M [auth A] Focus chain W [auth B] Focus chain YA [auth D] Interactions & Density Focus chain LA [auth C] Focus chain M [auth A] Focus chain W [auth B] Focus chain YA [auth D]