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- PDB-7zi3: Crystal structure of dCK C4S-S74E mutant in complex with UDP and ... -

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Basic information

Entry
Database: PDB / ID: 7zi3
TitleCrystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0642 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-J98 / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBen-Yaala, K. / Saez-Ayala, M. / 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)33,7764
Polymers32,7021
Non-polymers1,0743
Water1,17165
1
A: Deoxycytidine kinase
hetero molecules

A: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5518
Polymers65,4032
Non-polymers2,1486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4080 Å2
ΔGint-51 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.940, 68.940, 120.763
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-J98 / 2-[2-[[2-methyl-5-[4-(4-methylpiperazin-1-yl)sulfonyl-2-(trifluoromethyl)phenyl]phenyl]-propyl-amino]-1,3-thiazol-4-yl]pyrimidine-4,6-diamine


Mass: 646.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33F3N8O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#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.: 65 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978566 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978566 Å / Relative weight: 1
ReflectionResolution: 1.9→48.75 Å / Num. obs: 23515 / % possible obs: 99.9 % / Redundancy: 25.766 % / Biso Wilson estimate: 54.889 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.086 / Χ2: 0.767 / Net I/σ(I): 19.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.0226.9272.5931.1237000.6262.64299.8
2.02-2.1627.0841.242.6135070.8741.263100
2.16-2.3325.8670.6794.8832650.9590.692100
2.33-2.5526.5160.3619.530370.9860.368100
2.55-2.8526.9780.20317.2927550.9960.207100
2.85-3.2924.6460.10632.4924580.9980.108100
3.29-4.0324.1510.06752.3121020.9990.068100
4.03-5.6823.4410.05562.6416750.9990.056100
5.68-48.7521.010.04462.3610160.9970.04699.7

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Processing

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

4kcg


Resolution: 1.9→48.75 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.274 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1176 5 %RANDOM
Rwork0.1896 ---
obs0.1917 22339 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.79 Å2 / Biso mean: 51.899 Å2 / Biso min: 36.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0 Å2
2---0.33 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.9→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 70 65 2058
Biso mean--54.04 52.71 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132056
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151885
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.6612798
X-RAY DIFFRACTIONr_angle_other_deg1.3691.5854346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6115233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.61823.304115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69315362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5181511
X-RAY DIFFRACTIONr_chiral_restr0.0780.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
LS refinement shellResolution: 1.904→1.954 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 83 -
Rwork0.345 1590 -
all-1673 -
obs--99.46 %

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