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- PDB-4xhk: PIM1 kinase in complex with Compound 1s -

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Basic information

Entry
Database: PDB / ID: 4xhk
TitlePIM1 kinase in complex with Compound 1s
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / negative regulation of innate immune response / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / 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, ATP binding site ...Serine/threonine-protein kinase pim-1/2/3 / 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, 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-3YR / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMarcotte, D.J. / Silvian, L.F.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Structure-based design of low-nanomolar PIM kinase inhibitors.
Authors: Ishchenko, A. / Zhang, L. / Le Brazidec, J.Y. / Fan, J. / Chong, J.H. / Hingway, A. / Raditsis, A. / Singh, L. / Elenbaas, B. / Hong, V.S. / Marcotte, D. / Silvian, L. / Enyedy, I. / Chao, J.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / 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 / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Serine/threonine-protein kinase pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3692
Polymers35,9671
Non-polymers4021
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.990, 96.990, 80.772
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Detailsbiological unit is the same as asym.

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Components

#1: Protein Serine/threonine-protein kinase pim-1


Mass: 35966.891 Da / Num. of mol.: 1 / Fragment: Protein kinase domain residues 92-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3YR / 2-(2,6-difluorophenyl)-N-{4-[(3S)-pyrrolidin-3-yloxy]pyridin-3-yl}-1,3-thiazole-4-carboxamide


Mass: 402.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16F2N4O2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 0.1M BisTRIS pH 5.5, 0.2M NaCl, 1.5M Ammonium Sulfate
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33796 / % possible obs: 99.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.061 / Χ2: 1.761 / Net I/av σ(I): 31.721 / Net I/σ(I): 15 / Num. measured all: 170437
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.975.10.38433681.32399.5
1.97-2.055.10.25333851.28999.6
2.05-2.145.10.1834001.28699.8
2.14-2.255.10.14233931.33899.9
2.25-2.395.10.133731.41299.9
2.39-2.585.10.08534081.463100
2.58-2.845.10.07234051.75499.9
2.84-3.2550.06733932.87599
3.25-4.094.80.05333673.47398.5
4.09-505.10.02833041.54594.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XWS

1xws


Resolution: 1.9→29.11 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.299 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 1707 5.1 %RANDOM
Rwork0.1561 32050 --
obs0.1576 43013 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.81 Å2 / Biso mean: 30.688 Å2 / Biso min: 13.64 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 28 267 2500
Biso mean--25.05 40.49 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192302
X-RAY DIFFRACTIONr_bond_other_d0.0020.022149
X-RAY DIFFRACTIONr_angle_refined_deg2.1141.9643125
X-RAY DIFFRACTIONr_angle_other_deg0.96834927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6115268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61223.051118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24315376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0151521
X-RAY DIFFRACTIONr_chiral_restr0.130.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_mcbond_it2.6672.2431078
X-RAY DIFFRACTIONr_mcbond_other2.6572.241077
X-RAY DIFFRACTIONr_mcangle_it3.4393.3341344
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 110 -
Rwork0.208 2373 -
all-2483 -
obs--99.2 %
Refinement TLS params.Method: refined / Origin x: -8.627 Å / Origin y: 40.197 Å / Origin z: 1.705 Å
111213212223313233
T0.0193 Å2-0.008 Å2-0.0112 Å2-0.034 Å20.0029 Å2--0.0218 Å2
L0.4584 °20.2084 °2-0.0827 °2-0.5195 °2-0.1777 °2--0.6964 °2
S0.0551 Å °-0.0284 Å °-0.0049 Å °-0.017 Å °-0.0476 Å °-0.0075 Å °0.0498 Å °-0.0583 Å °-0.0075 Å °

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