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- PDB-2xey: Crystal structure of checkpoint kinase 1 (Chk1) in complex with i... -

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Basic information

Entry
Database: PDB / ID: 2xey
TitleCrystal structure of checkpoint kinase 1 (Chk1) in complex with inhibitors
ComponentsSERINE/THREONINE-PROTEIN KINASE CHK1
KeywordsTRANSFERASE / DNA REPAIR / CELL CYCLE
Function / homology
Function and homology information


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 / nucleus organization ...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 / nucleus organization / negative regulation of gene expression, epigenetic / 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 / positive regulation of cell cycle / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / condensed nuclear chromosome / replication fork / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Signaling by SCF-KIT / G2/M DNA damage checkpoint / cellular response to mechanical stimulus / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein phosphorylation / protein domain specific binding / intracellular membrane-bounded organelle / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA damage response / chromatin / apoptotic process / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Checkpoint kinase 1, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Checkpoint kinase 1, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-YVQ / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMatthews, T.P. / McHardy, T. / Klair, S. / Boxall, K. / Fisher, M. / Cherry, M. / Allen, C.E. / Addison, G.J. / Ellard, J. / Aherne, G.W. ...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.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2010
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. / Montfort, R.V. / 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. / Montfort, R.V. / Garrett, M.D. / Reader, J.C. / Collins, I.
#1: Journal: J.Med.Chem. / Year: 2009
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.
History
DepositionMay 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE CHK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3432
Polymers33,0431
Non-polymers3001
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.970, 65.660, 57.960
Angle α, β, γ (deg.)90.00, 93.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE CHK1 / CHECKPOINT KINASE 1 / CHEK1 / CHK1


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.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-YVQ / 3-(1H-INDOL-3-YL)-6-(1H-PYRAZOL-4-YL)IMIDAZO[1,2-A]PYRAZINE


Mass: 300.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.9 % / Description: NONE
Crystal growDetails: DL-MALIC ACID/PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→43.4 Å / Num. obs: 8638 / % possible obs: 92.4 % / Observed criterion σ(I): 1.5 / Redundancy: 2.5 % / Biso Wilson estimate: 41.62 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.5 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WMW

2wmw


Resolution: 2.7→43.395 Å / SU ML: 0.45 / σ(F): 1.38 / Phase error: 24.61 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2655 406 4.7 %
Rwork0.2194 --
obs0.2216 8616 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.791 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.6983 Å20 Å2-0.9163 Å2
2--0.5297 Å2-0 Å2
3---9.1686 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 23 11 2088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132128
X-RAY DIFFRACTIONf_angle_d1.2282884
X-RAY DIFFRACTIONf_dihedral_angle_d17.6788
X-RAY DIFFRACTIONf_chiral_restr0.106309
X-RAY DIFFRACTIONf_plane_restr0.012370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.09060.30071490.2532785X-RAY DIFFRACTION95
3.0906-3.89350.24871210.21012757X-RAY DIFFRACTION93
3.8935-43.40110.25161360.20262668X-RAY DIFFRACTION88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2870.28150.05931.08730.07010.0111-0.6895-0.08210.02530.6436-0.1304-0.5155-0.69010.0170.01110.9616-0.28980.29821.65150.01840.701510.1557-5.050833.1263
20.26260.0501-0.12990.0147-0.03850.09520.3857-0.82710.321-0.38230.2314-0.0989-0.17860.04120.01440.5328-0.0332-0.19590.7430.13970.53336.8636-5.061529.3615
30.23950.14450.10790.1776-0.0110.11210.1447-0.1332-0.06340.77260.0007-0.41620.20990.46350.06080.87810.2446-0.16981.0394-0.00170.167613.6189-8.013520.9618
42.0871-0.7639-0.03161.63030.09140.7736-0.4743-1.3518-0.21880.82950.4488-0.2808-0.01780.19650.16190.32980.135-0.09140.53950.05740.13511.7661-1.967217.6168
51.8232-0.137-0.00060.9460.04130.2052-0.184-0.5124-0.15740.3615-0.012-0.0080.13730.0418-0.06960.14840.047-0.0130.1077-0.01010.15656.12753.64676.8528
60.34970.39790.05071.02410.60990.344-0.1456-0.1482-0.21420.1540.0215-0.06670.06730.065-0.05720.07640.0210.01840.1143-0.0110.22236.5721-4.4259-4.8654
73.09012.3026-0.51124.05460.87660.7536-0.05920.56550.3702-0.41270.0230.4515-0.0934-0.0706-0.23290.15940.0009-0.02130.14950.01310.0517-3.54274.2038-8.7831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:13)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 14:32)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 33:51)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 52:97)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 98:160)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 161:213)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 214:269)

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