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- PDB-2ym5: Crystal structure of checkpoint kinase 1 (Chk1) in complex with i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ym5 | ||||||
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Title | Crystal structure of checkpoint kinase 1 (Chk1) in complex with inhibitors | ||||||
![]() | SERINE/THREONINE-PROTEIN KINASE CHK1 | ||||||
![]() | TRANSFERASE / DNA REPAIR | ||||||
Function / homology | ![]() negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / nucleus organization / cellular response to caffeine / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / signal transduction in response to DNA damage / Activation of ATR in response to replication stress / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of cell cycle / regulation of signal transduction by p53 class mediator / condensed nuclear chromosome / replication fork / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / G2/M DNA damage checkpoint / Signaling by SCF-KIT / cellular response to mechanical stimulus / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / Processing of DNA double-strand break ends / DNA replication / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein domain specific binding / protein phosphorylation / intracellular membrane-bounded organelle / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / DNA damage response / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Reader, J.C. / Matthews, T.P. / Klair, S. / Cheung, K.M.J. / Scanlon, J. / Proisy, N. / Addison, G. / Ellard, J. / Piton, N. / Taylor, S. ...Reader, J.C. / Matthews, T.P. / Klair, S. / Cheung, K.M.J. / Scanlon, J. / Proisy, N. / Addison, G. / Ellard, J. / Piton, N. / Taylor, S. / Cherry, M. / Fisher, M. / Boxall, K. / Burns, S. / Walton, M.I. / Westwood, I.M. / Hayes, A. / Eve, P. / Valenti, M. / Brandon, A.H. / Box, G. / vanMontfort, R.L.M. / Williams, D.H. / Aherne, G.W. / Raynaud, F.I. / Eccles, S.A. / Garrett, M.D. / Collins, I. | ||||||
![]() | ![]() Title: Structure-Guided Evolution of Potent and Selective Chk1 Inhibitors Through Scaffold Morphing. Authors: Reader, J.C. / Matthews, T.P. / Klair, S. / Cheung, K.M.J. / Scanlon, J. / Proisy, N. / Addison, G. / Ellard, J. / Piton, N. / Taylor, S. / Cherry, M. / Fisher, M. / Boxall, K. / Burns, S. / ...Authors: Reader, J.C. / Matthews, T.P. / Klair, S. / Cheung, K.M.J. / Scanlon, J. / Proisy, N. / Addison, G. / Ellard, J. / Piton, N. / Taylor, S. / Cherry, M. / Fisher, M. / Boxall, K. / Burns, S. / Walton, M.I. / Westwood, I.M. / Hayes, A. / Eve, P. / Valenti, M. / De Haven Brandon, A. / Box, G. / Van Montfort, R.L.M. / Williams, D.H. / Aherne, G.W. / Raynaud, F.I. / Eccles, S.A. / Garrett, M.D. / Collins, I. #1: ![]() Title: Identification of Inhibitors of Checkpoint Kinase 1 Through Template Screening. Authors: Matthews, T.P. / Klair, S. / Burns, S. / Boxall, K. / Cherry, M. / Fisher, M. / Westwood, I.M. / Walton, M.I. / Mchardy, T. / Cheung, K.J. / Van Montfort, R. / Williams, D. / Aherne, G.W. / ...Authors: Matthews, T.P. / Klair, S. / Burns, S. / Boxall, K. / Cherry, M. / Fisher, M. / Westwood, I.M. / Walton, M.I. / Mchardy, T. / Cheung, K.J. / Van Montfort, R. / Williams, D. / Aherne, G.W. / Garrett, M.D. / Reader, J. / Collins, I. #2: ![]() Title: Design and Evaluation of 3,6-Di(Hetero)Aryl Imidazo[1,2-A]Pyrazines as Inhibitors of Checkpoint and Other Kinases. Authors: Matthews, T.P. / Mchardy, T. / Klair, S. / Boxall, K. / Fisher, M. / Cherry, M. / Allen, C.E. / Addison, G.J. / Ellard, J. / Aherne, G.W. / Westwood, I.M. / Van Montfort, R. / Garrett, M.D. ...Authors: Matthews, T.P. / Mchardy, T. / Klair, S. / Boxall, K. / Fisher, M. / Cherry, M. / Allen, C.E. / Addison, G.J. / Ellard, J. / Aherne, G.W. / Westwood, I.M. / Van Montfort, R. / Garrett, M.D. / Reader, J.C. / Collins, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.7 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 792.8 KB | Display | ![]() |
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Full document | ![]() | 795.5 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ym3C ![]() 2ym4C ![]() 2ym6C ![]() 2ym7C ![]() 2ym8C ![]() 2wmwS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 33042.988 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O14757, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-YM5 / ( |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.15 % / Description: NONE |
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Crystal grow | Details: DL-MALIC ACID, PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Jun 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→43.5 Å / Num. obs: 19321 / % possible obs: 88.3 % / Observed criterion σ(I): 1.5 / Redundancy: 2.6 % / Biso Wilson estimate: 27.26 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.3 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WMW Resolution: 2.03→36.67 Å / SU ML: 0.27 / σ(F): 1.03 / Phase error: 21.74 / Stereochemistry target values: ML Details: RESIDUES 1-7, 17-21, 43-50, 77, 78, 271-289 ARE DISORDERED.
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.005 Å2 / ksol: 0.382 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→36.67 Å
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Refine LS restraints |
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LS refinement shell |
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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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