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- PDB-5fp6: Structure of cyclin-dependent kinase 2 with small-molecule ligand... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fp6 | ||||||
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Title | Structure of cyclin-dependent kinase 2 with small-molecule ligand 3-(4,7-dichloro-1H-indol-3-yl)prop-2-yn-1-ol (AT17833) in an alternate binding site. | ||||||
![]() | CYCLIN-DEPENDENT KINASE 2 | ||||||
![]() | TRANSFERASE / KINASE / MITOSIS / CELL CYCLE / FRAGMENT SCREENING / ALTERNATE BINDING SITE. | ||||||
Function / homology | ![]() Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jhoti, H. / Ludlow, R.F. / O'Reilly, M. / Saini, H.K. / Tickle, I.J. / Verdonk, M. | ||||||
![]() | ![]() Title: Detection of Secondary Binding Sites in Proteins Using Fragment Screening. Authors: Ludlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H. #1: ![]() Title: Identification of N-(4-Piperidinyl)-4-(2,6-Dichlorobenzoylamino)-1H-Pyrazole-3-Carboxamide (at7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and ...Title: Identification of N-(4-Piperidinyl)-4-(2,6-Dichlorobenzoylamino)-1H-Pyrazole-3-Carboxamide (at7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design. Authors: Wyatt, P.G. / Woodhead, A.J. / Berdini, V. / Boulstridge, J.A. / Carr, M.G. / Cross, D.M. / Davis, D.J. / Devine, L.A. / Early, T.R. / Feltell, R.E. / Lewis, E.J. / Mcmenamin, R.L. / ...Authors: Wyatt, P.G. / Woodhead, A.J. / Berdini, V. / Boulstridge, J.A. / Carr, M.G. / Cross, D.M. / Davis, D.J. / Devine, L.A. / Early, T.R. / Feltell, R.E. / Lewis, E.J. / Mcmenamin, R.L. / Navarro, E.F. / O'Brien, M.A. / O'Reilly, M. / Reule, M. / Saxty, G. / Seavers, L.C.A. / Smith, D. / Squires, M.S. / Trewartha, G. / Walker, M.T. / Woolford, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129 KB | Display | ![]() |
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PDB format | ![]() | 101.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.2 KB | Display | ![]() |
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Full document | ![]() | 441.7 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fp5SC ![]() 5fpdC ![]() 5fpeC ![]() 5fpmC ![]() 5fpnC ![]() 5fpoC ![]() 5fprC ![]() 5fpsC ![]() 5fptC ![]() 5fpyC S: Starting model for refinement C: citing same article ( |
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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: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | 3-(4,7-DICHLORO-1H-INDOL-3-YL)PROP-2-YN-1-OL (MFZ): ASTEX COMPOUND REGISTRY AT17833 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: PROTEIN CONCENTRATION: 13.6 MG/ML, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Dec 12, 2007 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→32.3 Å / Num. obs: 24694 / % possible obs: 94.3 % / Observed criterion σ(I): -3.7 / Biso Wilson estimate: 27.83 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2 / % possible all: 63.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5FP5 Resolution: 1.85→32.29 Å / Cor.coef. Fo:Fc: 0.9397 / Cor.coef. Fo:Fc free: 0.9269 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.15 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 30.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.264 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→32.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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