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Yorodumi- PDB-3ipy: X-Ray structure of Human Deoxycytidine Kinase in complex with an ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ipy | ||||||
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Title | X-Ray structure of Human Deoxycytidine Kinase in complex with an inhibitor | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Human Deoxycytidine Kinase / ATP-binding / Kinase / Nucleotide-binding / 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 / phosphorylation / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Tari, L.W. / Swanson, R.V. / Hunter, M. / Hoffman, I. / Stouch, T.R. / Carson, K.G. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Lead optimization and structure-based design of potent and bioavailable deoxycytidine kinase inhibitors. Authors: Jessop, T.C. / Tarver, J.E. / Carlsen, M. / Xu, A. / Healy, J.P. / Heim-Riether, A. / Fu, Q. / Taylor, J.A. / Augeri, D.J. / Shen, M. / Stouch, T.R. / Swanson, R.V. / Tari, L.W. / Hunter, M. ...Authors: Jessop, T.C. / Tarver, J.E. / Carlsen, M. / Xu, A. / Healy, J.P. / Heim-Riether, A. / Fu, Q. / Taylor, J.A. / Augeri, D.J. / Shen, M. / Stouch, T.R. / Swanson, R.V. / Tari, L.W. / Hunter, M. / Hoffman, I. / Keyes, P.E. / Yu, X.C. / Miranda, M. / Liu, Q. / Swaffield, J.C. / David Kimball, S. / Nouraldeen, A. / Wilson, A.G. / Foushee, A.M. / Jhaver, K. / Finch, R. / Anderson, S. / Oravecz, T. / Carson, K.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ipy.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ipy.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ipy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/3ipy ftp://data.pdbj.org/pub/pdb/validation_reports/ip/3ipy | HTTPS FTP |
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-Related structure data
Related structure data | 3ipxC 1p60S 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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Unit cell |
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-Components
#1: Protein | Mass: 28627.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27707, deoxycytidine kinase #2: Chemical | #3: Chemical | ChemComp-B87 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.66 % |
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Crystal grow | Details: 0.1 M sodium acetate, 25% PEG 4000, 8% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: May 7, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→119.52 Å / Num. all: 20090 / Num. obs: 20090 |
-Processing
Software | Name: REFMAC / Version: 5.2.0005 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P60 Resolution: 2.54→119.52 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / SU B: 10.258 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.543 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.486 Å2
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Refinement step | Cycle: LAST / Resolution: 2.54→119.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.54→2.609 Å / Total num. of bins used: 20
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