2VPP

Drosophila melanogaster deoxyribonucleoside kinase successfully activates gemcitabine in transduced cancer cell lines

PDB DOI: https://doi.org/10.2210/pdb2VPP/pdb

Classification: TRANSFERASE
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-03-03 Released: 2009-03-24
Deposition Author(s): Knecht, W., Mikkelsen, N.E., Clausen, A., Willer, M., Gojkovic, Z., Piskur, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.253
R-Value Work: 0.207
R-Value Observed: 0.209

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Drosophila Melanogaster Deoxyribonucleoside Kinase Activates Gemcitabine.

Knecht, W., Mikkelsen, N.E., Clausen, A., Willer, M., Eklund, H., Gojkovic, Z., Piskur, J.

(2009) Biochem Biophys Res Commun 382: 430

PubMed: 19285960 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2009.03.041
Primary Citation of Related Structures:
2VPP

PubMed Abstract:
Drosophila melanogaster multisubstrate deoxyribonucleoside kinase (Dm-dNK) can additionally sensitize human cancer cell lines towards the anti-cancer drug gemcitabine. We show that this property is based on the Dm-dNK ability to efficiently phosphorylate gemcitabine. The 2.2A resolution structure of Dm-dNK in complex with gemcitabine shows that the residues Tyr70 and Arg105 play a crucial role in the firm positioning of gemcitabine by extra interactions made by the fluoride atoms. This explains why gemcitabine is a good substrate for Dm-dNK.

Organizational Affiliation

BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark.

Macromolecule Content

Total Structure Weight: 54.53 kDa
Atom Count: 3,394
Modelled Residue Count: 371
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYNUCLEOSIDE KINASE	A, B	230	Drosophila melanogaster	Mutation(s): 0 EC: 2.7.1.145
UniProt
Find proteins for Q9XZT6 (Drosophila melanogaster) Explore Q9XZT6 Go to UniProtKB: Q9XZT6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9XZT6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GEO Query on GEO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	GEMCITABINE C₉ H₁₁ F₂ N₃ O₄ SDUQYLNIPVEERB-QPPQHZFASA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
GEO	PDBBind: 2VPP	IC50: 760 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.253
R-Value Work: 0.207
R-Value Observed: 0.209
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.106	α = 90
b = 62.298	β = 90
c = 68.078	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-03-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-24
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description