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- PDB-5tex: Pim-1 kinase in complex with a 7-azaindole -

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Basic information

Entry
Database: PDB / ID: 5tex
TitlePim-1 kinase in complex with a 7-azaindole
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTransferase/Transferase Inhibitor / KINASE / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / 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 / Signaling by FLT3 fusion proteins ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / 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 / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / 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 / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / negative regulation of apoptotic process / 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 ...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-7AU / IMIDAZOLE / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.149 Å
AuthorsMechin, I. / Wang, R. / Batchelor, J.D. / McLean, L.
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
DepositionSep 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 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)32,1073
Polymers31,6051
Non-polymers5022
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.536, 97.536, 81.104
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: 31604.873 Da / Num. of mol.: 1 / Fragment: UNP residues 33-306
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-7AU / (4-{4-chloro-1-methyl-2-[4-(piperazin-1-yl)phenyl]-1H-pyrrolo[2,3-b]pyridin-3-yl}phenyl)methanol


Mass: 432.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25ClN4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: imidazole 0,1M - NaAcetate 1M - pH6,5 / PH range: 6.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.149→37.46 Å / Num. obs: 23887 / % possible obs: 99.5 % / Redundancy: 13.5 % / Net I/σ(I): 3.67

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.149→37.46 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.87
RfactorNum. reflection% reflection
Rfree0.2167 1997 8.36 %
Rwork0.1813 --
obs0.1842 23887 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.149→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 36 123 2390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092331
X-RAY DIFFRACTIONf_angle_d1.0033165
X-RAY DIFFRACTIONf_dihedral_angle_d13.6351364
X-RAY DIFFRACTIONf_chiral_restr0.056332
X-RAY DIFFRACTIONf_plane_restr0.006411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1495-2.20320.2951380.27671533X-RAY DIFFRACTION99
2.2032-2.26280.27371420.26681540X-RAY DIFFRACTION100
2.2628-2.32940.26411410.23231549X-RAY DIFFRACTION100
2.3294-2.40460.29711430.21431567X-RAY DIFFRACTION100
2.4046-2.49050.27731460.21771562X-RAY DIFFRACTION100
2.4905-2.59020.26741440.2131540X-RAY DIFFRACTION100
2.5902-2.7080.25681460.22161591X-RAY DIFFRACTION100
2.708-2.85080.23651420.20421526X-RAY DIFFRACTION100
2.8508-3.02930.23451390.20021581X-RAY DIFFRACTION100
3.0293-3.26310.25331450.19671574X-RAY DIFFRACTION100
3.2631-3.59120.24651390.18271559X-RAY DIFFRACTION100
3.5912-4.11030.19161430.15941579X-RAY DIFFRACTION100
4.1103-5.17640.17971410.14921578X-RAY DIFFRACTION100
5.1764-37.46530.17061480.15981611X-RAY DIFFRACTION100

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