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- PDB-8r1t: Pim1 in complex with 4-(4-aminophenethyl)benzoic acid and Pimtide -

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Basic information

Entry
Database: PDB / ID: 8r1t
TitlePim1 in complex with 4-(4-aminophenethyl)benzoic acid and Pimtide
Components
  • Pimtide
  • Serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / SERINE KINASE / KINASE / COMPLEX / PIM1 / PIM / PIM-1 / INHIBITOR / TUMORIGENISIS / CANCER / PIMTIDE / PROTO ONCOGEN / ATP / PHOSPHORYLATION / APOPTOSIS / CELL CYCLE
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 / 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
Similarity search - Domain/homology
: / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHochban, P.M.M. / Heine, A. / Diederich, W.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arch Pharm / Year: 2024
Title: What doesn't fit is made to fit: Pim-1 kinase adapts to the configuration of stilbene-based inhibitors.
Authors: Hochban, P.M.M. / Heyder, L. / Heine, A. / Diederich, W.E.
History
DepositionNov 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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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
D: Pimtide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5974
Polymers37,2632
Non-polymers3332
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint3 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.007, 97.007, 80.295
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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


Mass: 35670.477 Da / Num. of mol.: 1 / Mutation: R250G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Protein/peptide Pimtide


Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-XIJ / 4-(4-aminophenethyl)benzoic acid / 4-[2-(4-aminophenyl)ethyl]benzoic acid


Mass: 241.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
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: 3.1 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM bis-tris-propane (pH 7.0), 10% ethylene glycol, 0.3% DMSO, 20% PEG3350, 200 mM Mg(OAc)2
PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2021
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→48.5 Å / Num. obs: 28946 / % possible obs: 99.4 % / Redundancy: 11.5 % / Biso Wilson estimate: 35.67 Å2 / CC1/2: 1 / Net I/σ(I): 29.2
Reflection shellResolution: 2→2.01 Å / Num. unique obs: 4616 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.20.1_4487refinement
XDS3.1.9data reduction
XDS3.1.9data scaling
PHASERphasing
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.22 Å / SU ML: 0.164 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.6059
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1795 1446 5 %
Rwork0.1589 27491 -
obs0.1599 28937 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.95 Å2
Refinement stepCycle: LAST / Resolution: 2→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 24 128 2398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732339
X-RAY DIFFRACTIONf_angle_d0.73853175
X-RAY DIFFRACTIONf_chiral_restr0.0542339
X-RAY DIFFRACTIONf_plane_restr0.0092422
X-RAY DIFFRACTIONf_dihedral_angle_d27.2759857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.20881430.17512705X-RAY DIFFRACTION98.61
2.07-2.150.18341440.16322733X-RAY DIFFRACTION99.55
2.15-2.250.20481430.15832730X-RAY DIFFRACTION98.9
2.25-2.370.19551440.14732734X-RAY DIFFRACTION99.38
2.37-2.520.16781450.15362757X-RAY DIFFRACTION99.55
2.52-2.710.19841440.16752734X-RAY DIFFRACTION99.62
2.71-2.980.21031450.16482753X-RAY DIFFRACTION99.08
2.99-3.420.18281460.16542771X-RAY DIFFRACTION99.83
3.42-4.30.15861450.14812757X-RAY DIFFRACTION99.55
4.3-36.220.17171470.16112817X-RAY DIFFRACTION99.36
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7367435314890.3569708835-0.3134315264930.173324657884-0.1525042449410.1336470377130.288519891818-0.3200907599820.03280958335140.201026159049-0.009773985541320.111123124740.220379670287-0.1346209913660.02350794021570.5532733443970.138695351305-0.1129424600970.4624952273220.03306842236650.3888337671105.083246177204.34259479215.3563743775
20.0587535891923-0.004542369957940.1436030728370.3752771986820.3170696989760.6538400698570.147026987150.0458032591779-0.3513843107750.157306485379-0.17336122538-0.397902221620.293465832280.2062661228130.001290971852870.2700552821350.0751230665409-0.03673008636820.4477269952940.03694204278860.529164619041123.741530824198.705407979-3.68944347354
30.166168682206-0.0684551544772-0.048547027010.058771261613-0.04202166933070.2308326504330.3777854656620.395017470776-0.0646050776198-0.518065841187-0.2852591277150.1355028824750.2471372441950.2496172101670.000219883624610.3645278557390.144571691637-0.03997000945880.444812677049-0.08527718073440.37463167713112.697431575197.832768675-12.0968530475
41.1346043041-0.415089738764-0.07239735366790.9945458551190.2752140773241.859962162210.01915966755-0.06375156366-0.05177343553970.168361226930.02559481137980.01711140882450.01328234188590.0133149559191.51963343531E-50.237093173358-0.0141737928199-0.01478580344830.2817858184890.01096946660190.250328658307100.621523657211.6187207482.41215824344
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 1 through 9 )DD1 - 91 - 9
22chain 'A' and (resid 33 through 73 )AA33 - 731 - 41
33chain 'A' and (resid 74 through 114 )AA74 - 11442 - 82
44chain 'A' and (resid 115 through 305 )AA115 - 30583 - 273

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