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

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Basic information

Entry
Database: PDB / ID: 7zia
TitleCrystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0634 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 / cytosol / cytoplasm
Similarity search - Function
Deoxynucleoside kinase / : / Deoxynucleoside kinase domain / Deoxynucleoside kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-J29 / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)33,7094
Polymers32,7021
Non-polymers1,0073
Water1,78399
1
A: Deoxycytidine kinase
hetero molecules

A: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4178
Polymers65,4032
Non-polymers2,0146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4060 Å2
ΔGint-51 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.003, 69.003, 121.166
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-J29 / 2-[2-[[2-methyl-5-[6-(4-methylpiperazin-1-yl)sulfonylpyridin-3-yl]phenyl]-propyl-amino]-1,3-thiazol-4-yl]pyrimidine-4,6-diamine


Mass: 579.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.9 M Sodium citrate, 60 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.7→48.79 Å / Num. obs: 32937 / % possible obs: 99.8 % / Redundancy: 25.053 % / Biso Wilson estimate: 44.045 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.058 / Χ2: 0.822 / Net I/σ(I): 28.58 / Num. measured all: 825173
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.821.1451.7891.47109067522151580.6911.83398.8
1.8-1.9326.8260.8863.65132011492149210.9270.903100
1.93-2.0827.220.4178.14125539461246120.9830.424100
2.08-2.2825.8990.20915.93110019424842480.9950.213100
2.28-2.5526.6950.1228.46103468387638760.9980.123100
2.55-2.9426.1760.07446.1589862343334330.9990.076100
2.94-3.624.7510.04871.64732132958295810.048100
3.6-5.0722.270.03887.78519112331233110.039100
5.07-48.7921.4880.03389.55300831409140010.03499.4

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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: 1.7→48.79 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.451 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 1647 5 %RANDOM
Rwork0.1868 ---
obs0.1885 31289 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.15 Å2 / Biso mean: 40.596 Å2 / Biso min: 21.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 1.7→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 66 99 2089
Biso mean--49.18 44.99 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132055
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151888
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.6632796
X-RAY DIFFRACTIONr_angle_other_deg1.4381.5854356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9065235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46523.246114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31215363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5721511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02485
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 116 -
Rwork0.314 2203 -
all-2319 -
obs--97.4 %

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