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- PDB-4q1d: Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 9... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4q1d | ||||||
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Title | Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 9 {2-{[(1R)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-propyl-1,3-thiazol-4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine} | ||||||
![]() | Deoxycytidine kinase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / PHOSPHORYL TRANSFER / PHOSPHORYLATION / DEOXYCYTIDINE / TRANSFERASE / INHIBITOR COMPLEX / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nomme, J. / Lavie, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.9 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4q18C ![]() 4q19C ![]() 4q1aC ![]() 4q1bC ![]() 4q1cC ![]() 4q1eC ![]() 4q1fC ![]() 4jlnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.53 % |
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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: 93 K | |||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 14, 2013 | |||||||||||||||
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→30 Å / Num. all: 37712 / Num. obs: 37712 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.033 / Net I/σ(I): 19.38 | |||||||||||||||
Reflection shell | Resolution: 2→2.12 Å / Mean I/σ(I) obs: 1.79 / Num. unique all: 6015 / Rsym value: 0.671 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4JLN Resolution: 2→27.39 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.218 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 / 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: 51.338 Å2
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Refinement step | Cycle: LAST / Resolution: 2→27.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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