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Yorodumi- PDB-4q1a: Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q1a | ||||||
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Title | Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 6 {2-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethanol} | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | TRANSFERASE/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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Nomme, J. / Lavie, A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q1a.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q1a.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 4q1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/4q1a ftp://data.pdbj.org/pub/pdb/validation_reports/q1/4q1a | HTTPS FTP |
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-Related structure data
Related structure data | 4q18C 4q19C 4q1bC 4q1cC 4q1dC 4q1eC 4q1fC 4jlnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.3 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 31, 2013 |
Radiation | Monochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 43643 / Num. obs: 43643 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.044 / Net I/σ(I): 20.64 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 62.9 % / Mean I/σ(I) obs: 2.54 / Num. unique all: 6955 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4JLN Resolution: 1.9→27.56 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.546 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.208 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→27.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.947 Å / Total num. of bins used: 20
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