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- PDB-4q1f: Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 1... -

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Basic information

Entry
Database: PDB / ID: 4q1f
TitleHuman dCK C4S-S74E mutant in complex with UDP and the inhibitor 12R {N-{2-[5-(4-{(1R)-1-[(4,6-diaminopyrimidin-2-yl)sulfanyl]ethyl}-5-methyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethyl}methanesulfonamide}
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PHOSPHORYL TRANSFER / PHOSPHORYLATION / DEOXYCYTIDINE / TRANSFERASE / INHIBITOR COMPLEX / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2XN / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNomme, J. / Lavie, A.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability.
Authors: Nomme, J. / Li, Z. / Gipson, R.M. / Wang, J. / Armijo, A.L. / Le, T. / Poddar, S. / Smith, T. / Santarsiero, B.D. / Nguyen, H.A. / Czernin, J. / Alexandrova, A.N. / Jung, M.E. / Radu, C.G. / Lavie, A.
History
DepositionApr 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxycytidine kinase
B: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2336
Polymers65,4032
Non-polymers1,8304
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-30 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.782, 68.782, 121.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Deoxycytidine kinase / dCK


Mass: 32701.627 Da / Num. of mol.: 2 / Mutation: C9S, C45S, C59S, S74E, C146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 C41 / References: UniProt: P27707, deoxycytidine kinase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-2XN / N-{2-[5-(4-{(1R)-1-[(4,6-diaminopyrimidin-2-yl)sulfanyl]ethyl}-5-methyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethyl}methanesulfonamide


Mass: 510.653 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N6O4S3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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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: 43.92 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M trisodium citrate dehydrate and 25 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 16, 2014
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 32727 / Num. obs: 32727 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.043 / Net I/σ(I): 21.66
Reflection shellResolution: 2.1→2.23 Å / Mean I/σ(I) obs: 2.12 / Num. unique all: 5224 / Rsym value: 0.756 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JLN

4jln


Resolution: 2.1→27.433 Å / σ(F): 1.34 / Phase error: 29.59 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1679 5.23 %random
Rwork0.2028 ---
obs0.2057 32133 97.77 %-
all-32133 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→27.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3794 0 116 170 4080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064006
X-RAY DIFFRACTIONf_angle_d1.0275444
X-RAY DIFFRACTIONf_dihedral_angle_d17.0621468
X-RAY DIFFRACTIONf_chiral_restr0.029580
X-RAY DIFFRACTIONf_plane_restr0.004678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16420.25471340.26562569X-RAY DIFFRACTION94
2.1642-2.23390.39731280.31492556X-RAY DIFFRACTION94
2.2339-2.31360.39581520.35112500X-RAY DIFFRACTION92
2.3136-2.4060.29751160.25322582X-RAY DIFFRACTION95
2.406-2.51520.32191380.25642543X-RAY DIFFRACTION94
2.5152-2.64730.36471320.25292586X-RAY DIFFRACTION94
2.6473-2.81250.33031350.25542505X-RAY DIFFRACTION94
2.8125-3.02870.25331370.23492571X-RAY DIFFRACTION94
3.0287-3.33150.24261270.22362536X-RAY DIFFRACTION93
3.3315-3.80920.24591520.18342508X-RAY DIFFRACTION92
3.8092-4.78270.1541390.14982511X-RAY DIFFRACTION92
4.7827-17.42660.17311570.16592432X-RAY DIFFRACTION88

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