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

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Basic information

Entry
Database: PDB / ID: 2wmt
TitleCrystal structure of checkpoint kinase 1 (Chk1) in complex with inhibitors
ComponentsSERINE/THREONINE-PROTEIN KINASE CHK1
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / POLYMORPHISM / PHOSPHOPROTEIN / UBL CONJUGATION / ISOPEPTIDE BOND / CHECKPOINT KINASE / NUCLEOTIDE-BINDING / SERINE/THREONINE KINASE / DNA DAMAGE / DNA REPAIR / ATP-BINDING / CHK1 / KINASE / NUCLEUS / CYTOPLASM / CELL CYCLE
Function / homology
Function and homology information


negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / regulation of mitotic centrosome separation / negative regulation of mitotic nuclear division / mitotic G2/M transition checkpoint / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / nucleus organization / negative regulation of gene expression, epigenetic ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / regulation of mitotic centrosome separation / negative regulation of mitotic nuclear division / mitotic G2/M transition checkpoint / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / nucleus organization / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / peptidyl-threonine phosphorylation / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / positive regulation of cell cycle / DNA damage checkpoint signaling / regulation of signal transduction by p53 class mediator / replication fork / condensed nuclear chromosome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / cellular response to mechanical stimulus / Signaling by SCF-KIT / G2/M DNA damage checkpoint / 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 / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein domain specific binding / protein serine kinase activity / DNA repair / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / DNA damage response / centrosome / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Checkpoint kinase 1, catalytic domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-ZYT / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMatthews, T.P. / Klair, S. / Burns, S. / Boxall, K. / Cherry, M. / Fisher, M. / Westwood, I.M. / Walton, M.I. / McHardy, T. / Cheung, K.-M.J. ...Matthews, T.P. / Klair, S. / Burns, S. / Boxall, K. / Cherry, M. / Fisher, M. / Westwood, I.M. / Walton, M.I. / McHardy, T. / Cheung, K.-M.J. / Van Montfort, R. / Williams, D. / Aherne, G.W. / Garrett, M.D. / Reader, J. / Collins, I.
CitationJournal: 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.-M.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.-M.J. / Van Montfort, R. / Williams, D. / Aherne, G.W. / Garrett, M.D. / Reader, J. / Collins, I.
History
DepositionJul 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,2692
Polymers33,0431
Non-polymers2261
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.830, 65.150, 53.990
Angle α, β, γ (deg.)90.00, 102.18, 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


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-ZYT / 2-(methylsulfanyl)-5-(thiophen-2-ylmethyl)-1H-imidazol-4-ol


Mass: 226.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2OS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.1 % / 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→32.6 Å / Num. obs: 9862 / % possible obs: 98.3 % / Observed criterion σ(I): 1.5 / Redundancy: 2.5 % / Biso Wilson estimate: 38.54 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.8
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7

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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 2HY0

2hy0


Resolution: 2.55→32.575 Å / SU ML: 0.38 / σ(F): 0.71 / Phase error: 25.82 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2566 811 4.7 %
Rwork0.2141 --
obs0.2162 17112 87.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.454 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 46.07 Å2
Baniso -1Baniso -2Baniso -3
1--9.1403 Å20 Å2-8.7517 Å2
2---2.8349 Å20 Å2
3---11.9752 Å2
Refinement stepCycle: LAST / Resolution: 2.55→32.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 14 50 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092068
X-RAY DIFFRACTIONf_angle_d1.2012805
X-RAY DIFFRACTIONf_dihedral_angle_d17.807759
X-RAY DIFFRACTIONf_chiral_restr0.08306
X-RAY DIFFRACTIONf_plane_restr0.006360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.70970.26321100.2672730X-RAY DIFFRACTION86
2.7097-2.91880.30991470.24572661X-RAY DIFFRACTION87
2.9188-3.21230.28081270.22852723X-RAY DIFFRACTION88
3.2123-3.67660.24481380.20672710X-RAY DIFFRACTION88
3.6766-4.630.19611330.16232735X-RAY DIFFRACTION88
4.63-32.57760.22061560.18122742X-RAY DIFFRACTION89
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)
10.3890.2494-0.54340.92520.26660.64570.02160.57220.0093-0.3757-0.01860.2171-0.0143-0.155-0.01190.41510.0191-0.11160.5097-0.05560.18655.656-1.07614.7641
22.4188-0.5176-0.6340.5820.03290.1440.0153-0.1835-0.0707-0.0356-0.05140.0477-0.03480.04320.04030.1833-0.0036-0.00090.15650.02010.167713.84833.466927.8591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 8:93)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 94:269)

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