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- PDB-6vru: PIM-inhibitor complex 1 -

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Basic information

Entry
Database: PDB / ID: 6vru
TitlePIM-inhibitor complex 1
ComponentsSerine/threonine-protein kinase pim-1
KeywordsONCOPROTEIN / TRANSFERASE/INHIBITOR / Inhibitor / complex / 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 / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response ...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 / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / positive regulation of TORC1 signaling / 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 / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / nucleolus / 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 / : / 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
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / Chem-ROY / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsBarberis, C.E. / Batchelor, J.D. / Mechin, I. / Liu, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Discovery of SARxxxx92, a pan-PIM kinase inhibitor, efficacious in a KG1 tumor model.
Authors: Barberis, C. / Erdman, P. / Czekaj, M. / Fire, L. / Pribish, J. / Tserlin, E. / Maniar, S. / Batchelor, J.D. / Liu, J. / Patel, V.F. / Hebert, A. / Levit, M. / Wang, A. / Sun, F. / Huang, S.A.
History
DepositionFeb 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 11, 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

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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)32,1004
Polymers31,6051
Non-polymers4953
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.555, 98.555, 81.009
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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
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-ROY / 3,4-dichloro-2-cyclopropyl-1-[(piperidin-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridine-6-carboxamide


Mass: 367.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20Cl2N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M imidazole, 0.7 M Na Acetate, pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 26194 / % possible obs: 95.8 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.09
Reflection shellResolution: 2.07→2.17 Å / Rmerge(I) obs: 0.95 / Num. unique obs: 1018

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Processing

Software
NameVersionClassification
CNSrefinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XR1

1xr1


Resolution: 2.07→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2024 1261 4.6 %
Rwork0.1786 --
obs-26194 95.8 %
Displacement parametersBiso max: 76.49 Å2 / Biso mean: 30.8185 Å2 / Biso min: 7.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å20.048 Å20 Å2
2---0.003 Å20 Å2
3---0.005 Å2
Refinement stepCycle: final / Resolution: 2.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 33 260 2517
Biso mean--29.56 42.2 -
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d0.852
X-RAY DIFFRACTIONc_mcbond_it1.4341.5
X-RAY DIFFRACTIONc_scbond_it2.3272
X-RAY DIFFRACTIONc_mcangle_it2.2852
X-RAY DIFFRACTIONc_scangle_it3.5872.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramimidazole.top
X-RAY DIFFRACTION2dna-rna_rep.paramSAR257479A.top
X-RAY DIFFRACTION3water_rep.paramacetate.top
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5imidazole.par
X-RAY DIFFRACTION6SAR257479A.par
X-RAY DIFFRACTION7acetate.par

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