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- PDB-5k4j: Crystal Structure of CDK2 in complex with compound 22 -

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Basic information

Entry
Database: PDB / ID: 5k4j
TitleCrystal Structure of CDK2 in complex with compound 22
ComponentsCyclin-dependent kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein Kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-6QB / Uncharacterized protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYin, J. / Wang, W.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery of (S)-1-(1-(4-Chloro-3-fluorophenyl)-2-hydroxyethyl)-4-(2-((1-methyl-1H-pyrazol-5-yl)amino)pyrimidin-4-yl)pyridin-2(1H)-one (GDC-0994), an Extracellular Signal-Regulated Kinase 1/2 ...Title: Discovery of (S)-1-(1-(4-Chloro-3-fluorophenyl)-2-hydroxyethyl)-4-(2-((1-methyl-1H-pyrazol-5-yl)amino)pyrimidin-4-yl)pyridin-2(1H)-one (GDC-0994), an Extracellular Signal-Regulated Kinase 1/2 (ERK1/2) Inhibitor in Early Clinical Development.
Authors: Blake, J.F. / Burkard, M. / Chan, J. / Chen, H. / Chou, K.J. / Diaz, D. / Dudley, D.A. / Gaudino, J.J. / Gould, S.E. / Grina, J. / Hunsaker, T. / Liu, L. / Martinson, M. / Moreno, D. / ...Authors: Blake, J.F. / Burkard, M. / Chan, J. / Chen, H. / Chou, K.J. / Diaz, D. / Dudley, D.A. / Gaudino, J.J. / Gould, S.E. / Grina, J. / Hunsaker, T. / Liu, L. / Martinson, M. / Moreno, D. / Mueller, L. / Orr, C. / Pacheco, P. / Qin, A. / Rasor, K. / Ren, L. / Robarge, K. / Shahidi-Latham, S. / Stults, J. / Sullivan, F. / Wang, W. / Yin, J. / Zhou, A. / Belvin, M. / Merchant, M. / Moffat, J. / Schwarz, J.B.
History
DepositionMay 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4882
Polymers34,0481
Non-polymers4411
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.646, 71.681, 72.197
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 Cyclin-dependent kinase 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 34047.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-6QB / 1-[(1~{S})-1-(4-chloranyl-3-fluoranyl-phenyl)-2-oxidanyl-ethyl]-4-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]pyridin-2-one


Mass: 440.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18ClFN6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4K, 50 mM Hepes pH7.5, 50 mM Ammonia Acetate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 37421 / % possible obs: 98.4 % / Redundancy: 4.3 % / Net I/σ(I): 12.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→36.912 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.76
RfactorNum. reflection% reflection
Rfree0.2231 3669 10.14 %
Rwork0.1751 --
obs0.18 36166 50.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→36.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 31 237 2536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222384
X-RAY DIFFRACTIONf_angle_d1.8893237
X-RAY DIFFRACTIONf_dihedral_angle_d14.083886
X-RAY DIFFRACTIONf_chiral_restr0.113360
X-RAY DIFFRACTIONf_plane_restr0.011412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5999-1.62090.2649960.2053887X-RAY DIFFRACTION36
1.6209-1.64310.27821050.19751091X-RAY DIFFRACTION43
1.6431-1.66660.20251280.19641140X-RAY DIFFRACTION46
1.6666-1.69150.26771450.19791174X-RAY DIFFRACTION49
1.6915-1.71790.24141600.19561226X-RAY DIFFRACTION50
1.7179-1.74610.2281340.19711258X-RAY DIFFRACTION51
1.7461-1.77620.24091530.18841239X-RAY DIFFRACTION51
1.7762-1.80850.22371440.18711260X-RAY DIFFRACTION52
1.8085-1.84330.25911730.19031264X-RAY DIFFRACTION52
1.8433-1.88090.2281570.17741255X-RAY DIFFRACTION52
1.8809-1.92180.23571550.17631263X-RAY DIFFRACTION52
1.9218-1.96650.2551470.17841245X-RAY DIFFRACTION51
1.9665-2.01570.19621200.17051297X-RAY DIFFRACTION52
2.0157-2.07020.2211510.16851263X-RAY DIFFRACTION52
2.0702-2.13110.21721640.17161265X-RAY DIFFRACTION52
2.1311-2.19990.20011280.16261278X-RAY DIFFRACTION52
2.1999-2.27850.21361190.17351291X-RAY DIFFRACTION52
2.2785-2.36970.19431340.16411291X-RAY DIFFRACTION52
2.3697-2.47750.20071350.16441297X-RAY DIFFRACTION52
2.4775-2.60810.18411310.16741277X-RAY DIFFRACTION52
2.6081-2.77150.24991440.1761291X-RAY DIFFRACTION53
2.7715-2.98540.25771510.18461322X-RAY DIFFRACTION53
2.9854-3.28560.26091280.18011333X-RAY DIFFRACTION54
3.2856-3.76060.20711470.16841313X-RAY DIFFRACTION54
3.7606-4.73640.18561750.14951277X-RAY DIFFRACTION53
4.7364-36.92180.25151450.19171400X-RAY DIFFRACTION57
Refinement TLS params.Method: refined / Origin x: -1.9553 Å / Origin y: -30.5706 Å / Origin z: 57.9652 Å
111213212223313233
T0.0273 Å20.0087 Å20.0019 Å2-0.0115 Å2-0.0147 Å2--0.0472 Å2
L0.7869 °20.355 °2-0.0178 °2-0.2315 °2-0.0672 °2--1.1023 °2
S0.0164 Å °0.0494 Å °-0.0342 Å °0.0127 Å °-0.016 Å °-0.0707 Å °-0.0189 Å °0.0027 Å °0.0005 Å °
Refinement TLS groupSelection details: chain A

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