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- PDB-5dia: PIM1 in complex with Cpd36 ((1S,3S)-N1-(6-(5-(pyridin-3-yl)-1H-py... -

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Basic information

Entry
Database: PDB / ID: 5dia
TitlePIM1 in complex with Cpd36 ((1S,3S)-N1-(6-(5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridin-3-yl)pyridin-2-yl)cyclohexane-1,3-diamine)
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTransferase/Transferase Inhibitor / PIM-1 / kinase / ATP-competitive / Structure-based drug design / 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 brown fat cell differentiation / positive regulation of TORC1 signaling / 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 / 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 / : / 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-5E6 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.964 Å
AuthorsMurray, J.M. / Wallweber, H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Discovery of 3,5-substituted 6-azaindazoles as potent pan-Pim inhibitors.
Authors: Hu, H. / Wang, X. / Chan, G.K. / Chang, J.H. / Do, S. / Drummond, J. / Ebens, A. / Lee, W. / Ly, J. / Lyssikatos, J.P. / Murray, J. / Moffat, J.G. / Chao, Q. / Tsui, V. / Wallweber, H. / Kolesnikov, A.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / 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 / _pdbx_struct_oper_list.symmetry_operation

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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)34,8332
Polymers34,4471
Non-polymers3851
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.0790, 97.0790, 80.6870
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 34447.141 Da / Num. of mol.: 1 / Fragment: kinase domain (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) / Strain (production host): BL21
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-5E6 / (1S,3S)-N-{6-[5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridin-3-yl]pyridin-2-yl}cyclohexane-1,3-diamine


Mass: 385.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23N7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4000, 0.2M LiSO4, 0.1M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.964→84.073 Å / Num. obs: 30084 / % possible obs: 97.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 34.801 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 30.2 / Num. measured all: 221504
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.964-1.9716.70.6453.1139720770.2
9.113-84.0735.40.019161229887.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALAdata scaling
PHASERphasing
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.964→37.28 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 1527 5.08 %random
Rwork0.196 ---
obs0.1976 30079 97.43 %-
Displacement parametersBiso max: 121.78 Å2 / Biso mean: 41.1516 Å2 / Biso min: 19.76 Å2
Refinement stepCycle: LAST / Resolution: 1.964→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 29 219 2460
LS refinement shellResolution: 1.964→2.0276 Å
RfactorNum. reflection% reflection
Rfree0.2752 124 5 %
Rwork0.2583 2119 -
obs--81 %

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