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

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Basic information

Entry
Database: PDB / ID: 2wmw
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


Activation of ATR in response to replication stress / Signaling by SCF-KIT / Processing of DNA double-strand break ends / Presynaptic phase of homologous DNA pairing and strand exchange / TP53 Regulates Transcription of DNA Repair Genes / Regulation of TP53 Activity through Phosphorylation / G2/M DNA damage checkpoint / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Transcriptional Regulation by E2F6 ...Activation of ATR in response to replication stress / Signaling by SCF-KIT / Processing of DNA double-strand break ends / Presynaptic phase of homologous DNA pairing and strand exchange / TP53 Regulates Transcription of DNA Repair Genes / Regulation of TP53 Activity through Phosphorylation / G2/M DNA damage checkpoint / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Transcriptional Regulation by E2F6 / regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage / histone kinase activity (H3-T11 specific) / negative regulation of mitotic nuclear division / regulation of histone H3-K9 acetylation / regulation of mitotic centrosome separation / chromatin-mediated maintenance of transcription / signal transduction involved in G2 DNA damage checkpoint / regulation of double-strand break repair via homologous recombination / DNA damage induced protein phosphorylation / negative regulation of G0 to G1 transition / replicative senescence / positive regulation of cell cycle / condensed nuclear chromosome / DNA damage checkpoint / chromatin / cellular response to mechanical stimulus / peptidyl-threonine phosphorylation / kinase activity / regulation of signal transduction by p53 class mediator / DNA replication / intracellular signal transduction / non-specific serine/threonine protein kinase / cell cycle / protein kinase activity / centrosome / intracellular membrane-bounded organelle / DNA repair / apoptotic process / cellular response to DNA damage stimulus / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Protein kinase domain / Checkpoint kinase 1, catalytic domain / Protein kinase-like domain superfamily / Serine/threonine-protein kinase, active site / Protein kinase domain / Protein kinases ATP-binding region signature. / Serine/Threonine protein kinases active-site signature. / Protein kinase domain profile. / Protein kinase, ATP binding site
Serine/threonine-protein kinase Chk1
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 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. / 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. / Garrett, M.D. / Reader, J. / Collins, I.
Validation Report
SummaryFull reportAbout validation report
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

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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)33,3552
Polymers33,0431
Non-polymers3121
Water1,51384
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)45.090, 65.890, 57.980
Angle α, β, γ (deg.)90.00, 94.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide 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-ZYW / 1-[(2S)-4-(5-BROMO-1H-PYRAZOLO[3,4-B]PYRIDIN-4-YL)MORPHOLIN-2-YL]METHANAMINE


Mass: 312.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14BrN5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / 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: 2.43→26.6 Å / Num. obs: 12064 / % possible obs: 94 % / Observed criterion σ(I): 1.5 / Redundancy: 2.4 % / Biso Wilson estimate: 35.73 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3
Reflection shellResolution: 2.43→2.56 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.7 / % possible all: 96.9

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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
Resolution: 2.43→26.575 Å / SU ML: 0.41 / σ(F): 0.63 / Phase error: 27.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2501 1007 4.8 %
Rwork0.2289 --
Obs0.2299 20911 83.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.656 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 45.59 Å2
Baniso -1Baniso -2Baniso -3
1--9.8646 Å20 Å2-1.2141 Å2
2--10.03 Å2-0 Å2
3----0.1654 Å2
Refinement stepCycle: LAST / Resolution: 2.43→26.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 18 84 2098
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0122062
f_angle_d1.0352795
f_dihedral_angle_d19.452762
f_chiral_restr0.08305
f_plane_restr0.008356
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4301-2.55810.34911530.3168283484
2.5581-2.71820.35251230.2741291784
2.7182-2.92780.29641400.2697285384
2.9278-3.2220.24911550.2571283783
3.222-3.68720.23191200.2139283083
3.6872-4.64150.181580.175282883
4.6415-26.57630.22451580.1936280583
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.22070.0808-0.23870.52490.03350.1968-0.1470.3181-0.02470.1143-0.0186-0.15860.3737-0.5090.14870.74520.0210.10010.6101-0.09840.412712.1233-2.8641-0.4135
20.9689-0.1155-0.28960.9105-0.24180.153-0.0210.0301-0.0507-0.0638-0.03920.04030.0205-0.05190.04970.11790.00030.00640.1247-0.00490.098915.76023.006426.7791
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection details
11(CHAIN A AND RESID 7:41)
22(CHAIN A AND RESID 42:269)

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