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

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Basic information

Entry
Database: PDB / ID: 5tel
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 / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation ...positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of brown fat cell differentiation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / regulation of transmembrane transporter activity / negative regulation of innate immune response / regulation of mitotic cell cycle / protein serine/threonine kinase activator activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / protein autophosphorylation / Interleukin-4 and Interleukin-13 signaling / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-7AJ / IMIDAZOLE / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.214 Å
AuthorsMechin, I. / Wang, R. / Batchelor, J.D.
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 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,1283
Polymers31,6051
Non-polymers5232
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.474, 97.474, 80.788
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-7AJ / 4-chloro-2-{5,6-dimethoxy-1-[2-(4-methylpiperazin-1-yl)ethyl]-1H-indol-3-yl}-1H-pyrrolo[2,3-b]pyridine


Mass: 453.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28ClN5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: imidazole 0,1M - NaAcetate 0,7M - pH6,5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.214→31.101 Å / Num. obs: 20718 / % possible obs: 95 % / Redundancy: 13.5 % / Net I/σ(I): 43

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155:)refinement
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YXT

1yxt


Resolution: 2.214→31.101 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 21.03
RfactorNum. reflection% reflection
Rfree0.2071 1990 9.61 %
Rwork0.1788 --
obs0.1816 20718 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.214→31.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 37 159 2423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032339
X-RAY DIFFRACTIONf_angle_d0.6983177
X-RAY DIFFRACTIONf_dihedral_angle_d12.7341374
X-RAY DIFFRACTIONf_chiral_restr0.045333
X-RAY DIFFRACTIONf_plane_restr0.004411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2145-2.26980.25141240.22511144X-RAY DIFFRACTION81
2.2698-2.33120.25431240.2081262X-RAY DIFFRACTION90
2.3312-2.39980.24551340.2041285X-RAY DIFFRACTION92
2.3998-2.47720.24141410.20091287X-RAY DIFFRACTION92
2.4772-2.56570.22521450.19841303X-RAY DIFFRACTION93
2.5657-2.66840.23961430.19911322X-RAY DIFFRACTION94
2.6684-2.78970.271460.20661358X-RAY DIFFRACTION96
2.7897-2.93670.23481400.18931355X-RAY DIFFRACTION97
2.9367-3.12060.21291480.19431358X-RAY DIFFRACTION98
3.1206-3.36120.22311490.18481395X-RAY DIFFRACTION99
3.3612-3.6990.20141510.17081402X-RAY DIFFRACTION100
3.699-4.23310.19611470.16631411X-RAY DIFFRACTION99
4.2331-5.32890.17081450.15411406X-RAY DIFFRACTION99
5.3289-31.10360.1781530.1691440X-RAY DIFFRACTION100

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