8OOJ | pdb_00008ooj

Crystal structure of dCK C4S-S74E mutant in complex with EdC and UDP

PDB DOI: https://doi.org/10.2210/pdb8OOJ/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Bacteria
Mutation(s): Yes

Deposited: 2023-04-05 Released: 2023-12-20
Deposition Author(s): Saez-Ayala, M., Rebuffet, E., Betzi, S., Morelli, X.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.279 (Depositor), 0.282 (DCC)
R-Value Work:
0.237 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

4'-Ethynyl-2'-Deoxycytidine (EdC) Preferentially Targets Lymphoma and Leukemia Subtypes by Inducing Replicative Stress.

Calbert, M.L., Chandramouly, G., Adams, C.M., Saez-Ayala, M., Kent, T., Tyagi, M., Ayyadevara, V.S.S.A., Wang, Y., Krais, J.J., Gordon, J., Atkins, J., Toma, M.M., Betzi, S., Boghossian, A.S., Rees, M.G., Ronan, M.M., Roth, J.A., Goldman, A.R., Gorman, N., Mitra, R., Childers, W.E., Grana, X., Skorski, T., Johnson, N., Hurtz, C., Morelli, X., Eischen, C.M., Pomerantz, R.T.

(2024) Mol Cancer Ther 23: 683-699

PubMed: 38064712 Search on PubMed
DOI: https://doi.org/10.1158/1535-7163.MCT-23-0487
Primary Citation Related Structures:
8OOJ

PubMed Abstract:
Anticancer nucleosides are effective against solid tumors and hematologic malignancies, but typically are prone to nucleoside metabolism resistance mechanisms. Using a nucleoside-specific multiplexed high-throughput screening approach, we discovered 4'-ethynyl-2'-deoxycytidine (EdC) as a third-generation anticancer nucleoside prodrug with preferential activity against diffuse large B-cell lymphoma (DLBCL) and acute lymphoblastic leukemia (ALL). EdC requires deoxycytidine kinase (DCK) phosphorylation for its activity and induces replication fork arrest and accumulation of cells in S-phase, indicating it acts as a chain terminator. A 2.1Å cocrystal structure of DCK bound to EdC and UDP reveals how the rigid 4'-alkyne of EdC fits within the active site of DCK. Remarkably, EdC was resistant to cytidine deamination and SAMHD1 metabolism mechanisms and exhibited higher potency against ALL compared with FDA-approved nelarabine. Finally, EdC was highly effective against DLBCL tumors and B-ALL in vivo. These data characterize EdC as a preclinical nucleoside prodrug candidate for DLBCL and ALL.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.

Macromolecule Content

Total Structure Weight: 133.43 kDa
Atom Count: 8,016
Modeled Residue Count: 928
Deposited Residue Count: 1,120
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxycytidine kinase	A, B, C, D	280	Homo sapiens	Mutation(s): 5 Gene Names: DCK EC: 2.7.1.74 (PDB Primary Data), 2.7.1.76 (PDB Primary Data), 2.7.1.113 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P27707 (Homo sapiens) Explore P27707 Go to UniProtKB: P27707
PHAROS: P27707 GTEx: ENSG00000156136
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27707
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
VVC (Subject of Investigation/LOI) Query on VVC Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	4-azanyl-1-[(2~{R},4~{S},5~{R})-5-ethynyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one C₁₁ H₁₃ N₃ O₄ MSPJPGIGNWYLAC-JVUFJMBOSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]