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- PDB-2b54: Human cyclin dependent kinase 2 (CKD2)complexed with DIN-232305 -

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Basic information

Entry
Database: PDB / ID: 2b54
TitleHuman cyclin dependent kinase 2 (CKD2)complexed with DIN-232305
ComponentsCell division protein kinase 2
KeywordsTRANSFERASE / PROTEIN KINASE / CELL CYCLE / PHOSPHORYLATION / CELL DIVISION / MITOSIS / INHIBITION
Function / homology
Function and homology information


Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-D05 / Uncharacterized protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChang, C.-C.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Synthesis and biological evaluation of 1-aryl-4,5-dihydro-1h-pyraxolo[3,4-d]pyrimidin-4-one inhibitors of cyclin dependent kinases
Authors: Markwalder, J.A. / Arnone, M.R. / Benfield, P.A. / Boisclair, M. / Burton, C.R. / Chang, C.-C. / Cox, S.S. / Czerniak, P.M. / Dean, C.L. / Dolenaik, D. / Grafstrom, R. / Harrison, B.A. / ...Authors: Markwalder, J.A. / Arnone, M.R. / Benfield, P.A. / Boisclair, M. / Burton, C.R. / Chang, C.-C. / Cox, S.S. / Czerniak, P.M. / Dean, C.L. / Dolenaik, D. / Grafstrom, R. / Harrison, B.A. / Kaltenbach III, R.F. / Nugiel, D.A. / Rossi, K.A. / Sherk, S.R. / Sisk, L.M. / Stouten, P. / Trainor, G.L. / Worland, P. / Seitz, S.P.
History
DepositionSep 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4422
Polymers33,9761
Non-polymers4661
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.970, 73.160, 54.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell division protein kinase 2 / p33 protein kinase / CDK2


Mass: 33976.488 Da / Num. of mol.: 1
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: P24941, EC: 2.7.1.37
#2: Chemical ChemComp-D05 / 6-(3,4-DIHYDROXYBENZYL)-3-ETHYL-1-(2,4,6-TRICHLOROPHENYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4(5H)-ONE / DIN-232305


Mass: 465.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15Cl3N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100mM HEPES pH 7.4, 50mM Ammonium Acetate, 2mM DTT, 4-14% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 26, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→37.44 Å / Num. obs: 21779 / % possible obs: 83.7 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 3.1
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 0.5 / % possible all: 67.3

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Processing

Software
NameVersionClassification
PROCESS(RIGAKU)data collection
SCALE(RIGAKU)data reduction
X-PLORmodel building
CNX2002refinement
PROCESS(RIGAKU)data reduction
SCALE(RIGAKU)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE CDK2 MODEL

Resolution: 1.85→37.44 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 411647.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.263 838 9.9 %RANDOM
Rwork0.158 ---
obs-20039 78 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0684 Å2 / ksol: 0.225363 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--2.65 Å20 Å2
3----1.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 1.85→37.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 30 318 3259
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.154
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg9.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d30.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d8.27
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.891.5
X-RAY DIFFRACTIONc_mcangle_it3.252
X-RAY DIFFRACTIONc_scbond_it142
X-RAY DIFFRACTIONc_scangle_it13.872.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.085 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 22 11.7 %
Rwork0.354 166 -
obs--4.5 %
Xplor fileSerial no: 1 / Param file: wat21_cnx.xprm

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