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- PDB-7zi2: Crystal structure of dCK C4S-S74E mutant in complex with UDP and ... -

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Basic information

Entry
Database: PDB / ID: 7zi2
TitleCrystal structure of dCK C4S-S74E mutant in complex with UDP and the dCKi2 inhibitor
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / Inhibitor
Function / homology
Function and homology information


deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity ...deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity / pyrimidine nucleotide metabolic process / Purine salvage / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
Deoxynucleoside kinase / : / Deoxynucleoside kinase domain / Deoxynucleoside kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-J7W / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsSaez-Ayala, M. / Ben-Yaala, K. / Betzi, S. / Rebuffet, E. / Morelli, X.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation ARCSL220130606659 France
CitationJournal: Nat Commun / Year: 2023
Title: From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia.
Authors: Saez-Ayala, M. / Hoffer, L. / Abel, S. / Ben Yaala, K. / Sicard, B. / Andrieu, G.P. / Latiri, M. / Davison, E.K. / Ciufolini, M.A. / Bremond, P. / Rebuffet, E. / Roche, P. / Derviaux, C. / ...Authors: Saez-Ayala, M. / Hoffer, L. / Abel, S. / Ben Yaala, K. / Sicard, B. / Andrieu, G.P. / Latiri, M. / Davison, E.K. / Ciufolini, M.A. / Bremond, P. / Rebuffet, E. / Roche, P. / Derviaux, C. / Voisset, E. / Montersino, C. / Castellano, R. / Collette, Y. / Asnafi, V. / Betzi, S. / Dubreuil, P. / Combes, S. / Morelli, X.
History
DepositionApr 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6584
Polymers32,7021
Non-polymers9573
Water66737
1
A: Deoxycytidine kinase
hetero molecules

A: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3178
Polymers65,4032
Non-polymers1,9146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4110 Å2
ΔGint-50 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.836, 68.836, 123.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Deoxycytidine kinase / dCK / Deoxyadenosine kinase / Deoxyguanosine kinase


Mass: 32701.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Production host: Escherichia coli (E. coli)
References: UniProt: P27707, deoxycytidine kinase, 2'-deoxyadenosine kinase, deoxyguanosine kinase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-J7W / N-[3-[[4-[4,6-bis(azanyl)pyrimidin-2-yl]-1,3-thiazol-2-yl]amino]-4-methyl-phenyl]-4-[(4-methylpiperazin-1-yl)methyl]benzamide


Mass: 529.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31N9OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 0.9 M Sodium Citrate, 60 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.18→60.14 Å / Num. obs: 16221 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 43.966 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.126 / Net I/σ(I): 10.1 / Num. measured all: 174047
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
2.18-2.2211.21.191108100.5811.959
5.92-60.178.923.483579400.020.061

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCG

4kcg


Resolution: 2.18→48.72 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.193 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 749 4.6 %RANDOM
Rwork0.2013 ---
obs0.2041 15419 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.77 Å2 / Biso mean: 52.838 Å2 / Biso min: 33.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2---1.47 Å20 Å2
3---2.95 Å2
Refinement stepCycle: final / Resolution: 2.18→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 64 37 2024
Biso mean--59.79 45.18 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132035
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151872
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6642760
X-RAY DIFFRACTIONr_angle_other_deg1.2971.5864309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5075227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70123.246114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28815358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3531511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
LS refinement shellResolution: 2.181→2.238 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 57 -
Rwork0.371 1107 -
all-1164 -
obs--100 %

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