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- PDB-3bgz: Human Pim-1 kinase in complex with diphenyl indole inhibitor VX3 -

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Basic information

Entry
Database: PDB / ID: 3bgz
TitleHuman Pim-1 kinase in complex with diphenyl indole inhibitor VX3
ComponentsProto-oncogene serine/threonine-protein kinase Pim-1
KeywordsTRANSFERASE / kinase inhibitor phosphorylation / Alternative initiation / ATP-binding / Cytoplasm / Manganese / Membrane / Metal-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Proto-oncogene / Serine/threonine-protein kinase
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / 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 / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / 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 / 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 / cytoplasm / cytosol
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
2,3-diphenyl-1H-indole-7-carboxylic acid / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsJacobs, M.D.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Docking study yields four novel inhibitors of the protooncogene pim-1 kinase.
Authors: Pierce, A.C. / Jacobs, M. / Stuver-Moody, C.
History
DepositionNov 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Proto-oncogene serine/threonine-protein kinase Pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2972
Polymers37,9841
Non-polymers3131
Water2,018112
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.130, 98.130, 80.800
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 Proto-oncogene serine/threonine-protein kinase Pim-1


Mass: 37984.074 Da / Num. of mol.: 1 / Fragment: kinase domain residues 92-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pBEV1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 pLysS
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-VX3 / 2,3-diphenyl-1H-indole-7-carboxylic acid


Mass: 313.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H15NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 58.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1 M ammonium phosphate dibasic, 100 mM citrate, 200 mM sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→19.52 Å / Num. obs: 17322 / % possible obs: 99.9 % / Redundancy: 7.43 % / Rmerge(I) obs: 0.081 / Χ2: 0.96 / Net I/σ(I): 12.1 / Scaling rejects: 973
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.4-2.497.460.413.81291417051.4499.7
2.49-2.587.460.3364.31305917291.2899.8
2.58-2.77.50.2725.11303717191.2399.7
2.7-2.847.480.2136.41293517121.1199.9
2.84-3.027.50.158.51314917410.9699.9
3.02-3.257.480.10511.41310217410.8599.9
3.25-3.587.490.07116.31282017050.7499.9
3.58-4.097.430.05619.71314217620.69100
4.09-5.147.280.04922.51264617330.6699.9
5.14-19.527.230.04623.61285617750.6399.8

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
d*TREKdata reduction
CNX2005refinement
RefinementResolution: 2.4→19.52 Å / Rfactor Rfree error: 0.008 / FOM work R set: 0.837 / Data cutoff high absF: 93581.602 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 815 4.8 %RANDOM
Rwork0.194 ---
obs0.196 16833 96.9 %-
all-17308 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.259 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å23.45 Å20 Å2
2--0.36 Å20 Å2
3----0.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 24 112 2326
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.52
X-RAY DIFFRACTIONc_mcbond_it0.721.5
X-RAY DIFFRACTIONc_mcangle_it1.292
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 122 4.5 %
Rwork0.245 2563 -
all-2685 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3inhib.par&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4ion.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5parmxray.xpl&_1_TOPOLOGY_INFILE_5

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