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Yorodumi- PDB-5fp6: Structure of cyclin-dependent kinase 2 with small-molecule ligand... -
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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. | ||||||
Components | CYCLIN-DEPENDENT KINASE 2 | ||||||
Keywords | TRANSFERASE / KINASE / MITOSIS / CELL CYCLE / FRAGMENT SCREENING / ALTERNATE BINDING SITE. | ||||||
Function / homology | Function and homology information cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation ...cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / telomere maintenance in response to DNA damage / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / G0 and Early G1 / Telomere Extension By Telomerase / Activation of the pre-replicative complex / cellular response to nitric oxide / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / cyclin-dependent protein kinase holoenzyme complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / : / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / DNA replication / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / transcription regulator complex / chromosome, telomeric region / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA-templated transcription / centrosome / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Jhoti, H. / Ludlow, R.F. / O'Reilly, M. / Saini, H.K. / Tickle, I.J. / Verdonk, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 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: Journal: J.Med.Chem. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fp6.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fp6.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fp6_validation.pdf.gz | 440.2 KB | Display | wwPDB validaton report |
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Full document | 5fp6_full_validation.pdf.gz | 441.7 KB | Display | |
Data in XML | 5fp6_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5fp6_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fp6 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fp6 | 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 (ref.) |
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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: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24941, cyclin-dependent kinase | ||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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