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- PDB-2ycq: Crystal structure of checkpoint kinase 2 in complex with inhibito... -

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Basic information

Entry
Database: PDB / ID: 2ycq
TitleCrystal structure of checkpoint kinase 2 in complex with inhibitor PV1115
ComponentsSERINE/THREONINE-PROTEIN KINASE CHK2
KeywordsTRANSFERASE / ANTICANCER DRUG DESIGN
Function / homology
Function and homology information


mitotic DNA damage checkpoint signaling / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage ...mitotic DNA damage checkpoint signaling / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / protein catabolic process / G2/M DNA damage checkpoint / PML body / Regulation of TP53 Activity through Methylation / cellular response to gamma radiation / intrinsic apoptotic signaling pathway in response to DNA damage / G2/M transition of mitotic cell cycle / Regulation of TP53 Degradation / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ubiquitin protein ligase binding / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / 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 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-UPX / Serine/threonine-protein kinase Chk2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)37,0283
Polymers36,5621
Non-polymers4652
Water2,936163
1
A: SERINE/THREONINE-PROTEIN KINASE CHK2
hetero molecules

A: SERINE/THREONINE-PROTEIN KINASE CHK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0556
Polymers73,1242
Non-polymers9314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2990 Å2
ΔGint-12.1 kcal/mol
Surface area29140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.039, 91.039, 93.320
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-UPX / N-{4-[(1E)-N-1H-IMIDAZOL-2-YLETHANEHYDRAZONOYL]PHENYL}-7-NITRO-1H-INDOLE-2-CARBOXAMIDE


Mass: 403.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17N7O3
#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.: 163 / 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 NITRATE, 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-BM / 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: 2.05→50 Å / Num. obs: 26596 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.3
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.6 / % possible all: 95.9

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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: 2.05→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.911 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24729 1330 5.1 %RANDOM
Rwork0.20915 ---
obs0.2111 24780 91.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å20 Å2
2---0.24 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 34 163 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222360
X-RAY DIFFRACTIONr_bond_other_d0.0010.021622
X-RAY DIFFRACTIONr_angle_refined_deg1.32423187
X-RAY DIFFRACTIONr_angle_other_deg0.863.0023973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2345285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1552598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10315445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.334159
X-RAY DIFFRACTIONr_chiral_restr0.0780.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
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_it0.6691.51425
X-RAY DIFFRACTIONr_mcbond_other0.1461.5574
X-RAY DIFFRACTIONr_mcangle_it1.23722306
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7753935
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8814.5880
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: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 112 -
Rwork0.258 1882 -
obs--94.77 %
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)
14.65243.07040.50632.10710.24980.35550.0789-0.3644-0.0402-0.0301-0.1367-0.04640.2101-0.04460.05780.1531-0.0056-0.00110.2157-0.01250.1384-56.3766-12.6473-3.7292
23.31160.63770.27372.54290.43262.4713-0.00890.3504-0.3365-0.1804-0.0681-0.01280.1388-0.11650.0770.16240.04340.00890.1689-0.05530.1069-38.1293-8.9109-9.4134
30.83050.32980.09391.34271.30332.2230.04510.0172-0.121-0.0674-0.1046-0.1351-0.06450.1150.05960.12550.00970.02240.10290.02490.1738-26.0326-4.08456.2799
40.96080.30470.01781.973-0.280.5949-0.09110.35960.235-0.1369-0.1182-0.3454-0.18370.22440.20940.0421-0.02010.02250.14880.11820.0633-30.0411-1.0415-14.7635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A211 - 300
2X-RAY DIFFRACTION2A301 - 374
3X-RAY DIFFRACTION3A375 - 448
4X-RAY DIFFRACTION4A449 - 510

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