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- PDB-4rvm: CHK1 kinase domain with diazacarbazole compound 19 -

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Basic information

Entry
Database: PDB / ID: 4rvm
TitleCHK1 kinase domain with diazacarbazole compound 19
ComponentsSerine/threonine-protein kinase Chk1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / phosphotransfer catalyst / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of G0 to G1 transition / apoptotic process involved in development / negative regulation of DNA biosynthetic process / 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 / negative regulation of gene expression, epigenetic / nucleus organization ...negative regulation of G0 to G1 transition / apoptotic process involved in development / negative regulation of DNA biosynthetic process / 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 / negative regulation of gene expression, epigenetic / nucleus organization / cellular response to caffeine / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / 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 / peptidyl-threonine phosphorylation / DNA damage checkpoint signaling / condensed nuclear chromosome / regulation of signal transduction by p53 class mediator / replication fork / TP53 Regulates Transcription of DNA Repair Genes / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / chromatin remodeling / protein domain specific binding / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / apoptotic process / centrosome / DNA damage response / 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-3X7 / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsGazzard, L. / Blackwood, E. / Burton, B. / Chapman, K. / Chen, H. / Crackett, P. / Drobnick, J. / Ellwood, C. / Epler, J. / Flagella, M. ...Gazzard, L. / Blackwood, E. / Burton, B. / Chapman, K. / Chen, H. / Crackett, P. / Drobnick, J. / Ellwood, C. / Epler, J. / Flagella, M. / Goodacre, S. / Halladay, J. / Hunt, H. / Kintz, S. / Lyssikatos, J. / MacLeod, C. / Ramiscal, S. / Schmidt, S. / Seward, E. / Wiesmann, C. / Williams, K. / Wu, P. / Yee, S. / Yen, I. / Malek, S.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Mitigation of Acetylcholine Esterase Activity in the 1,7-Diazacarbazole Series of Inhibitors of Checkpoint Kinase 1.
Authors: Gazzard, L. / Williams, K. / Chen, H. / Axford, L. / Blackwood, E. / Burton, B. / Chapman, K. / Crackett, P. / Drobnick, J. / Ellwood, C. / Epler, J. / Flagella, M. / Gancia, E. / Gill, M. / ...Authors: Gazzard, L. / Williams, K. / Chen, H. / Axford, L. / Blackwood, E. / Burton, B. / Chapman, K. / Crackett, P. / Drobnick, J. / Ellwood, C. / Epler, J. / Flagella, M. / Gancia, E. / Gill, M. / Goodacre, S. / Halladay, J. / Hewitt, J. / Hunt, H. / Kintz, S. / Lyssikatos, J. / Macleod, C. / Major, S. / Medard, G. / Narukulla, R. / Ramiscal, J. / Schmidt, S. / Seward, E. / Wiesmann, C. / Wu, P. / Yee, S. / Yen, I. / Malek, S.
History
DepositionNov 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)34,5732
Polymers34,2051
Non-polymers3671
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.123, 65.930, 58.117
Angle α, β, γ (deg.)90.00, 94.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase Chk1 / CHK1 checkpoint homolog / Cell cycle checkpoint kinase / Checkpoint kinase-1


Mass: 34205.199 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 1-289)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3X7 / 3-[4-(piperidin-1-ylmethyl)phenyl]-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile


Mass: 367.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Hepes, isopropanol, PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 3, 2008
RadiationMonochromator: varimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→20 Å / Num. all: 28744 / Num. obs: 23800 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.057 / Net I/σ(I): 20.6

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Processing

Software
NameVersionClassification
JDirectordata collection
AMoREphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZYS

1zys


Resolution: 1.86→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.855 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.17 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24248 1182 5 %RANDOM
Rwork0.20125 ---
obs0.20337 22482 82.78 %-
all-28744 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.269 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20.02 Å2
2--0.74 Å20 Å2
3----0.04 Å2
Refine analyzeLuzzati sigma a obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.86→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 28 148 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222227
X-RAY DIFFRACTIONr_bond_other_d0.0010.022023
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9813016
X-RAY DIFFRACTIONr_angle_other_deg0.83134721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02824.34106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87515395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8361514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
X-RAY DIFFRACTIONr_nbd_refined0.1980.2392
X-RAY DIFFRACTIONr_nbd_other0.1750.21966
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21056
X-RAY DIFFRACTIONr_nbtor_other0.0810.21240
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2124
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.212
X-RAY DIFFRACTIONr_mcbond_it3.8162.51724
X-RAY DIFFRACTIONr_mcbond_other0.7012.5531
X-RAY DIFFRACTIONr_mcangle_it4.552132
X-RAY DIFFRACTIONr_scbond_it3.2522.51129
X-RAY DIFFRACTIONr_scangle_it4.5225884
LS refinement shellResolution: 1.86→1.898 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.931 73 -
Rwork0.589 1318 -
obs--84.35 %
Refinement TLS params.Method: refined / Origin x: 5.5315 Å / Origin y: 11.804 Å / Origin z: 6.4334 Å
111213212223313233
T-0.0159 Å2-0.0087 Å2-0.0006 Å2--0.0396 Å2-0.0069 Å2---0.0196 Å2
L0.7425 °2-0.0677 °2-0.2632 °2-0.285 °20.0342 °2--0.7779 °2
S-0.025 Å °-0.0522 Å °-0.0215 Å °0.0408 Å °-0.0197 Å °0.0203 Å °0.0691 Å °0.0371 Å °0.0446 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A401 - 548
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A3 - 273

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