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- PDB-4n6y: Pim1 Complexed with a phenylcarboxamide -

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Basic information

Entry
Database: PDB / ID: 4n6y
TitlePim1 Complexed with a phenylcarboxamide
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 / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / 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 / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / 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 / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / 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 / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of 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 / Protein kinase, ATP binding site ...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-2HV / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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

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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)37,9412
Polymers37,5971
Non-polymers3441
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.875, 97.875, 80.454
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-2HV / 2-(acetylamino)-N-[2-(piperidin-1-yl)phenyl]-1,3-thiazole-4-carboxamide


Mass: 344.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.96 Å3/Da / Density % sol: 58.43 %
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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13638 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 50.47 Å2 / Rmerge(I) obs: 0.178 / Net I/σ(I): 10.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
BUSTER2.11.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→22.2 Å / Cor.coef. Fo:Fc: 0.9481 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 671 4.95 %RANDOM
Rwork0.1565 ---
obs0.1592 13554 100 %-
Displacement parametersBiso mean: 37.29 Å2
Baniso -1Baniso -2Baniso -3
1--2.2442 Å20 Å20 Å2
2---2.2442 Å20 Å2
3---4.4884 Å2
Refine analyzeLuzzati coordinate error obs: 0.256 Å
Refinement stepCycle: LAST / Resolution: 2.6→22.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 24 211 2459
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012329HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.113182HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d802SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes356HARMONIC5
X-RAY DIFFRACTIONt_it2329HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion18.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion279SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2819SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.81 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2844 139 4.99 %
Rwork0.1972 2648 -
all0.2014 2787 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 30.8034 Å / Origin y: 27.5888 Å / Origin z: 0.1209 Å
111213212223313233
T-0.0488 Å20.0126 Å2-0.0285 Å2--0.0533 Å20.0261 Å2---0.1553 Å2
L1.6187 °2-0.3775 °2-0.1051 °2-1.0687 °20.0969 °2--1.6928 °2
S-0.055 Å °-0.1392 Å °0.0438 Å °-0.0171 Å °0.1307 Å °0.0746 Å °-0.0172 Å °-0.1054 Å °-0.0757 Å °
Refinement TLS groupSelection details: { A|32 - A|305 }

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