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- PDB-2ycs: Crystal structure of checkpoint kinase 2 in complex with PV788 -

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Basic information

Entry
Database: PDB / ID: 2ycs
TitleCrystal structure of checkpoint kinase 2 in complex with PV788
ComponentsSERINE/THREONINE-PROTEIN KINASE CHK2
KeywordsTRANSFERASE / ANTICANCER DRUG DESIGN
Function / homology
Function and homology information


positive regulation of anoikis / mitotic DNA damage checkpoint signaling / cellular response to bisphenol A / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / response to glycoside / thymocyte apoptotic process / cellular response to stress / regulation of protein catabolic process / negative regulation of DNA damage checkpoint ...positive regulation of anoikis / mitotic DNA damage checkpoint signaling / cellular response to bisphenol A / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / response to glycoside / thymocyte apoptotic process / cellular response to stress / regulation of protein catabolic process / negative regulation of DNA damage checkpoint / replicative senescence / signal transduction in response to DNA damage / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / mitotic spindle assembly / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage checkpoint signaling / regulation of signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / protein catabolic process / cellular response to gamma radiation / PML body / G2/M DNA damage checkpoint / Regulation of TP53 Activity through Methylation / G2/M transition of mitotic cell cycle / cellular response to xenobiotic stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / Regulation of TP53 Degradation / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein autophosphorylation / Regulation of TP53 Activity through Phosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein stabilization / cell division / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / DNA damage response / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site ...Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Chem-NXP / Serine/threonine-protein kinase Chk2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLountos, G.T. / Jobson, A.G. / Tropea, J.E. / Self, C.R. / Pommier, Y. / Shoemaker, R.H. / Zhang, G. / Waugh, D.S.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structural Characterization of Inhibitor Complexes with Checkpoint Kinase 2 (Chk2), a Drug Target for Cancer Therapy.
Authors: Lountos, G.T. / Jobson, A.G. / Tropea, J.E. / Self, C.R. / Zhang, G. / Pommier, Y. / Shoemaker, R.H. / Waugh, D.S.
History
DepositionMar 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 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

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE CHK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9593
Polymers36,5621
Non-polymers3962
Water2,216123
1
A: SERINE/THREONINE-PROTEIN KINASE CHK2
hetero molecules

A: SERINE/THREONINE-PROTEIN KINASE CHK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9176
Polymers73,1242
Non-polymers7934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2910 Å2
ΔGint-13.4 kcal/mol
Surface area28910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.203, 91.203, 92.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE CHK2 / CHECKPOINT KINASE 2 / CDS1


Mass: 36562.238 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 210-531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PDZ1927 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: O96017, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NXP / N-{4-[(1E)-N-CARBAMIMIDOYLETHANEHYDRAZONOYL]PHENYL}-1H-INDOLE-3-CARBOXAMIDE


Mass: 334.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N6O
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.05 Å3/Da / Density % sol: 59.7 % / Description: NONE
Crystal growpH: 7.8
Details: 0.1M HEPES PH 7.8, 0.1M MAGNESIUM SULFATE, 14% W/V PEG 3350, 16% V/V ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 19012 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 41.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0104refinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CN5

2cn5


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 13.421 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23899 980 5.2 %RANDOM
Rwork0.20032 ---
obs0.20226 18003 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.342 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 29 123 2404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222340
X-RAY DIFFRACTIONr_bond_other_d0.0010.021601
X-RAY DIFFRACTIONr_angle_refined_deg1.5252.0043159
X-RAY DIFFRACTIONr_angle_other_deg0.84933930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2215279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70824.94897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44315440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.537159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212511
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7131.51405
X-RAY DIFFRACTIONr_mcbond_other0.1341.5564
X-RAY DIFFRACTIONr_mcangle_it1.36422275
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0353935
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3134.5883
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.347→2.408 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 77 -
Rwork0.258 1231 -
obs--94.99 %
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)
15.7362-2.96780.38161.9674-0.34820.6249-0.2573-0.31750.0080.19010.2332-0.01550.0888-0.13050.02410.2270.033-0.03060.21440.00240.1595-39.52542.748412.0986
22.3783-0.69920.55992.07790.14441.94170.03560.1531-0.1709-0.2309-0.06910.2101-0.1038-0.08650.03340.21060.0174-0.04040.1587-0.02730.161-27.268628.68915.9734
30.9571-0.12970.94830.75360.5921.9581-0.06380.0163-0.1611-0.06570.01220.0713-0.00310.11920.05160.1686-0.00060.0510.1684-0.00540.2551-16.90620.071421.4791
42.19370.1156-0.06612.295-0.69750.37590.02760.3211-0.1815-0.4006-0.1767-0.370.09560.23640.14910.20790.01280.07350.26830.02360.0744-16.324225.65670.5482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A210 - 300
2X-RAY DIFFRACTION2A301 - 374
3X-RAY DIFFRACTION3A375 - 448
4X-RAY DIFFRACTION4A449 - 510

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