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- PDB-4n70: Pim1 Complexed with a pyridylcarboxamide -

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Basic information

Entry
Database: PDB / ID: 4n70
TitlePim1 Complexed with a pyridylcarboxamide
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / phosphorylation / 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 / 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 / : / 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-2HX / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBellamacina, C.R. / Le, V. / Shu, W. / Burger, M.T. / Bussiere, D.
CitationJournal: ACS Med Chem Lett / Year: 2013
Title: Structure Guided Optimization, in Vitro Activity, and in Vivo Activity of Pan-PIM Kinase Inhibitors.
Authors: Burger, M.T. / Han, W. / Lan, J. / Nishiguchi, G. / Bellamacina, C. / Lindval, M. / Atallah, G. / Ding, Y. / Mathur, M. / McBride, C. / Beans, E.L. / Muller, K. / Tamez, V. / Zhang, Y. / ...Authors: Burger, M.T. / Han, W. / Lan, J. / Nishiguchi, G. / Bellamacina, C. / Lindval, M. / Atallah, G. / Ding, Y. / Mathur, M. / McBride, C. / Beans, E.L. / Muller, K. / Tamez, V. / Zhang, Y. / Huh, K. / Feucht, P. / Zavorotinskaya, T. / Dai, Y. / Holash, J. / Castillo, J. / Langowski, J. / Wang, Y. / Chen, M.Y. / Garcia, P.D.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)38,0542
Polymers37,5971
Non-polymers4571
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.950, 97.950, 81.080
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: 37596.703 Da / Num. of mol.: 1 / Fragment: UNP residues 93-404
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 DE3
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-2HX / N-{4-[(3R,4R,5S)-3-amino-4-hydroxy-5-methylpiperidin-1-yl]pyridin-3-yl}-6-(2,6-difluorophenyl)-5-fluoropyridine-2-carboxamide


Mass: 457.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22F3N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: RESERVOIR SOLUTION - 0.7M (NH4)2HPO4, 0.3M NACL, 0.1M NACITRATE, PH 5.5, PROTEIN SOLUTION - 7.5MG/ML IN 20MM HEPES, 100MM NACL, 5MM DTT, PH 8, COMPOUND WAS SOAKED IN, TEMPERATURE 298.0K, ...Details: RESERVOIR SOLUTION - 0.7M (NH4)2HPO4, 0.3M NACL, 0.1M NACITRATE, PH 5.5, PROTEIN SOLUTION - 7.5MG/ML IN 20MM HEPES, 100MM NACL, 5MM DTT, PH 8, COMPOUND WAS SOAKED IN, TEMPERATURE 298.0K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.1→42.41 Å / Num. obs: 25905 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 0.089
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3779 / Rsym value: 0.191 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.41 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 1317 5.09 %Random
Rwork0.1673 ---
obs0.1694 25888 99.93 %-
all-25905 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.767 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3284 Å2-0 Å2-0 Å2
2--3.3284 Å2-0 Å2
3----6.6567 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 33 234 2506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144530
X-RAY DIFFRACTIONf_angle_d1.378165
X-RAY DIFFRACTIONf_dihedral_angle_d15.9661141
X-RAY DIFFRACTIONf_chiral_restr0.103336
X-RAY DIFFRACTIONf_plane_restr0.008690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.22911390.18682760X-RAY DIFFRACTION100
2.1841-2.28350.20871500.17252694X-RAY DIFFRACTION100
2.2835-2.40390.1921330.15212731X-RAY DIFFRACTION100
2.4039-2.55440.20351360.15162717X-RAY DIFFRACTION100
2.5544-2.75160.20691560.15662716X-RAY DIFFRACTION100
2.7516-3.02850.22511560.16692722X-RAY DIFFRACTION100
3.0285-3.46650.22141520.16912712X-RAY DIFFRACTION100
3.4665-4.36680.18541620.14672735X-RAY DIFFRACTION100
4.3668-42.42220.19081330.16432784X-RAY DIFFRACTION99

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