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- PDB-5kcx: Pim-1 kinase in Complex with a Selective N-substituted 7-azaindol... -

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Basic information

Entry
Database: PDB / ID: 5kcx
TitlePim-1 kinase in Complex with a Selective N-substituted 7-azaindole Inhibitor
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/INHIBITOR / kinase / inhibitor / complex / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / 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 / cytoplasm / cytosol
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-6S3 / ACETATE ION / IMIDAZOLE / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsMechin, I. / McLean, L.R. / Zhang, Y. / Wang, R.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Discovery of N-substituted 7-azaindoles as PIM1 kinase inhibitors - Part I.
Authors: Barberis, C. / Moorcroft, N. / Arendt, C. / Levit, M. / Moreno-Mazza, S. / Batchelor, J. / Mechin, I. / Majid, T.
History
DepositionJun 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,1304
Polymers33,6181
Non-polymers5123
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.010, 98.010, 80.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 33618.105 Da / Num. of mol.: 1 / Fragment: UNP residues 120-404
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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Chemical ChemComp-6S3 / 4-chloranyl-1-methyl-2-[4-(4-methylpiperazin-1-yl)phenyl]pyrrolo[2,3-b]pyridine-6-carboxamide


Mass: 383.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22ClN5O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.49 Å3/Da / Density % sol: 63.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: protein stock: 6.26 mg/mL in Tris 20mM - DTT 5mM - NaCl 150mM - 0.5 mM inhibitor - pH8 crystallization solution: imidazole 0.1M - Na Acetate 0.6M - pH6.5 1:1 protein to solution ratio for ...Details: protein stock: 6.26 mg/mL in Tris 20mM - DTT 5mM - NaCl 150mM - 0.5 mM inhibitor - pH8 crystallization solution: imidazole 0.1M - Na Acetate 0.6M - pH6.5 1:1 protein to solution ratio for hanging drop freezing conditions: imidazole 0.1M - Na Acetate 1M - glycerol 20% - pH6.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42 Å / Num. obs: 21552 / % possible obs: 96 % / Redundancy: 4 % / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
CNX2005refinement
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
RefinementResolution: 2.2→42 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2112 1080 5 %
Rwork0.1902 --
obs-20474 96 %
Refinement stepCycle: LAST / Resolution: 2.2→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 36 143 2396

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