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- PDB-6kzi: Crystal structure of Ser/Thr kinase Pim1 in complex with thiorida... -

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Basic information

Entry
Database: PDB / ID: 6kzi
TitleCrystal structure of Ser/Thr kinase Pim1 in complex with thioridazine derivatives
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/INHIBITOR / Pim1 / 10-DEBC / 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-RTX / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, W. / Wan, X. / Li, W. / Xie, Y. / Huang, N.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences2011CB812402 China
Citation
Journal: J.Chem.Inf.Model. / Year: 2020
Title: Structure-Based Optimization of 10-DEBC Derivatives as Potent and Selective Pim-1 Kinase Inhibitors.
Authors: Li, G. / Zhang, W. / Xie, Y. / Li, Y. / Cao, R. / Zheng, G. / Huang, N. / Zhou, Y.
#1: Journal: To Be Published
Title: More than just a GPCR ligand: structure-based discovery of thioridazine derivatives as Pim-1 kinase inhibitors.
Authors: Li, W. / Wan, X. / Zeng, F. / Xie, Y. / Wang, Y. / Zhang, W. / Li, L. / Huang, N.
History
DepositionSep 24, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 4, 2020ID: 4MED
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6382
Polymers33,2931
Non-polymers3451
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Biological assembly 1 assigned by authors and generated by PISA (software)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13090 Å2
Unit cell
Length a, b, c (Å)98.925, 98.925, 80.830
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: 33292.719 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-RTX / 4-(2-chloro-10H-phenoxazin-10-yl)-N,N-diethylbutan-1-amine / 10-DEBC


Mass: 344.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25ClN2O / Feature type: SUBJECT OF INVESTIGATION
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: 3.61 Å3/Da / Density % sol: 65.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.4M potassium sodium tartrate tetrahydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→58.79 Å / Num. obs: 10591 / % possible obs: 99.57 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 0
Reflection shellResolution: 2.801→2.874 Å / Rmerge(I) obs: 0.178 / Num. unique obs: 787

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→58.79 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.976 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.579 / ESU R Free: 0.307
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 528 4.7 %RANDOM
Rwork0.1701 ---
obs0.1732 10591 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 151.18 Å2 / Biso mean: 53.627 Å2 / Biso min: 32.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.19 Å20 Å2
2---0.37 Å2-0 Å2
3---1.21 Å2
Refinement stepCycle: final / Resolution: 2.8→58.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 24 0 2252
Biso mean--60.38 --
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192314
X-RAY DIFFRACTIONr_bond_other_d0.0040.022172
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.9623141
X-RAY DIFFRACTIONr_angle_other_deg1.1233.0044986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8565272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70523.136118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83615379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4291521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212596
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02567
LS refinement shellResolution: 2.801→2.874 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 27 -
Rwork0.373 787 -
all-814 -
obs--98.43 %

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