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- PDB-7qfm: Pim1 in complex with (E)-4-((2-oxoindolin-3-ylidene)methyl)benzoi... -

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Basic information

Entry
Database: PDB / ID: 7qfm
TitlePim1 in complex with (E)-4-((2-oxoindolin-3-ylidene)methyl)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 / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of transmembrane transporter activity / 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 protein serine/threonine kinase activity ...positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of transmembrane transporter activity / 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 protein serine/threonine kinase activity / : / positive regulation of cardiac muscle cell proliferation / positive regulation of brown fat cell differentiation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / regulation of mitotic cell cycle / negative regulation of innate immune response / protein serine/threonine kinase activator activity / cellular response to type II interferon / manganese ion binding / protein autophosphorylation / Interleukin-4 and Interleukin-13 signaling / protein phosphorylation / non-specific serine/threonine protein kinase / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / 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
Chem-AY3 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHochban, P.M.M. / Heine, A. / Diederich, W.E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Pose, duplicate, then elaborate: Steps towards increased affinity for inhibitors targeting the specificity surface of the Pim-1 kinase.
Authors: Heyder, L. / Hochban, P.M.M. / Taylor, C. / Chevillard, F. / Siefker, C. / Iking, C. / Borchardt, H. / Aigner, A. / Klebe, G. / Heine, A. / Kolb, P. / Diederich, W.E.
History
DepositionDec 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_entity_src_syn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)37,5344
Polymers37,1762
Non-polymers3572
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint3 kcal/mol
Surface area12620 Å2
Unit cell
Length a, b, c (Å)96.818, 96.818, 80.147
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: 35583.398 Da / Num. of mol.: 1 / Mutation: R250G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pLIC-SGC / 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.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-AY3 / 4-[(~{E})-(2-oxidanylidene-1~{H}-indol-3-ylidene)methyl]benzoic acid


Mass: 265.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.1 Å3/Da / Density % sol: 59.7 %
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 MgOAc
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: Oct 23, 2020 / Details: Sagitally bended Si111-crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→48.409 Å / Num. obs: 31177 / % possible obs: 99.7 % / Redundancy: 20.7 % / Biso Wilson estimate: 34.91 Å2 / CC1/2: 1 / Rsym value: 0.038 / Net I/σ(I): 50
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 21 % / Mean I/σ(I) obs: 7.8 / Num. unique obs: 4980 / CC1/2: 1 / Rsym value: 0.44 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MxCuBEdata collection
XDS1.02data reduction
XDS1.02data scaling
Coot0.7.1model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NDT

5ndt


Resolution: 1.95→41.92 Å / SU ML: 0.145 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.2189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1779 1556 4.99 %
Rwork0.1583 29596 -
obs0.1593 31152 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.25 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 26 123 2345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672316
X-RAY DIFFRACTIONf_angle_d0.7853147
X-RAY DIFFRACTIONf_chiral_restr0.0539339
X-RAY DIFFRACTIONf_plane_restr0.005428
X-RAY DIFFRACTIONf_dihedral_angle_d21.23911373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.1871380.16052638X-RAY DIFFRACTION98.37
2.01-2.080.17431400.14612671X-RAY DIFFRACTION99.61
2.08-2.170.17971410.14822681X-RAY DIFFRACTION99.72
2.17-2.260.17851410.1582686X-RAY DIFFRACTION99.93
2.26-2.380.15991410.15182673X-RAY DIFFRACTION99.54
2.38-2.530.20121410.16132701X-RAY DIFFRACTION99.93
2.53-2.730.18841420.17072687X-RAY DIFFRACTION99.96
2.73-30.1811420.16752704X-RAY DIFFRACTION100
3-3.440.18621420.16212698X-RAY DIFFRACTION99.65
3.44-4.330.16721430.15072711X-RAY DIFFRACTION99.93
4.33-41.920.17681450.15952746X-RAY DIFFRACTION99.42
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)
10.8652172382230.04222265832940.210935880170.241390367441-0.09852442304920.492829268112-0.1506172258730.547168299505-0.0500016634972-0.03858694129460.22274528165-0.306653817663-0.1690956945460.4049562251050.000144009431840.380252986699-0.1072112011180.01846517216460.468447006176-0.02984221758260.477885022199-111.907906765201.102242541-8.57846559787
20.82228825180.1977622868330.6551571728690.284197404932-0.1239764123710.8565434959920.130413046262-0.01293837166160.369176734830.1828143025860.0285232788645-0.114119543413-0.4029384669130.2725311934320.00704516938070.354425024653-0.06576304909270.006820524084360.314558976863-0.01459189331380.344287018066-121.039892326203.173365297-3.3136298864
31.687417588150.161437291373-0.4536004574170.7996302024250.1891149970522.40321695575-0.0129520338311-0.0437729931992-0.02074778238680.06682950709970.0540551606524-0.0266419645660.111307453036-0.07529577251090.0001260593003870.241023465946-0.0341414522863-0.02440504934140.160461962501-0.007189023531140.198967813345-134.161464307191.1464773240.750284015915
40.250280592357-0.227199914557-0.3663578780941.61837108507-0.2467510945840.7739862233640.0343281944168-0.342460547965-0.3115395610080.8549014474020.3015266437030.008788118978540.5138807442970.3234757030620.01495366245170.429120657107-0.0386425060188-0.1022348976270.577954072229-0.03346975682620.379593173987-123.65150589192.79218957412.8723187049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 305 )
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 9 )

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