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- PDB-7qb2: Pim1 in complex with (E)-4-((6-amino-1-methyl-2-oxoindolin-3-ylid... -

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Basic information

Entry
Database: PDB / ID: 7qb2
TitlePim1 in complex with (E)-4-((6-amino-1-methyl-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-A7X / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsHochban, P.M.M. / Heine, A. / Diederich, W.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionNov 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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)37,5634
Polymers37,1762
Non-polymers3862
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint3 kcal/mol
Surface area12920 Å2
Unit cell
Length a, b, c (Å)97.785, 97.785, 80.188
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-A7X / 4-[(E)-(6-azanyl-1-methyl-2-oxidanylidene-indol-3-ylidene)methyl]benzoic acid / (E)-4-((6-amino-1-methyl-2-oxoindolin-3-ylidene)methyl)benzoic acid


Mass: 294.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 60.5 %
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: Mar 12, 2021 / 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: 2.53→48.893 Å / Num. obs: 14667 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 39.56 Å2 / CC1/2: 1 / Rsym value: 0.08 / Net I/σ(I): 28.3
Reflection shellResolution: 2.53→2.68 Å / Redundancy: 11.68 % / Mean I/σ(I) obs: 5.38 / Num. unique obs: 2355 / CC1/2: 0.959 / Rsym value: 0.526 / % possible all: 99.4

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Processing

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

5ndt


Resolution: 2.53→48.89 Å / SU ML: 0.2101 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.0239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2019 734 5.01 %
Rwork0.1571 13928 -
obs0.1593 14662 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.5 Å2
Refinement stepCycle: LAST / Resolution: 2.53→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 28 87 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722285
X-RAY DIFFRACTIONf_angle_d0.80453096
X-RAY DIFFRACTIONf_chiral_restr0.0537328
X-RAY DIFFRACTIONf_plane_restr0.0059420
X-RAY DIFFRACTIONf_dihedral_angle_d19.81721352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.720.24621450.17522747X-RAY DIFFRACTION99.42
2.72-30.19651460.16452767X-RAY DIFFRACTION99.97
3-3.430.21911460.15592786X-RAY DIFFRACTION100
3.43-4.320.17291470.1442790X-RAY DIFFRACTION99.97
4.32-48.890.20811500.16152838X-RAY DIFFRACTION99.9
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)
10.38993409950.5759034289410.116414382611.105362364490.4286382954241.4367459478-0.302962219862-0.07544451423140.152123438613-0.5359578838950.311920554527-0.114193285856-0.6127483792490.2554871018760.02566668212910.5448610772350.0812578134760.002404930504250.3279333808630.04944315809330.424703071986-36.83035453033.23439589139-2.19848002847
20.1674460723550.1834172796470.3636326217360.8070027488850.3810305140690.9188851652610.0476110931684-0.01443693176410.3145096029970.1417594664810.2098282160270.317320981436-0.536157836605-0.3423041705030.04052582782120.3350851285230.041506571160.006261532803560.2420935025710.00560933817770.283442361847-43.1139424613-3.593117739172.88062262852
30.8343181021420.0959034775249-0.5271785602691.244069310790.02307705776062.255343310670.03911272850140.01979404672140.003113963059710.0879836388718-0.0164157829317-0.05983195885580.2067175176770.00242252822874-3.24615959097E-50.2795131023120.0219372303457-0.02911010627310.2574108513980.002436718496890.277280187421-39.080579739-20.92465406946.80590625764
40.01841443854560.01147338862750.01840312870190.01217533743440.01394843140120.0149862664163-0.095305930835-0.254295414414-0.04309573273460.1305943837020.205815491809-0.129215462363-0.05168198852320.247547809544-0.0001240198786860.47817402046-0.0157455308812-0.01044820711180.402861455947-0.0972474404330.403675421631-35.7837519333-11.082548321619.1579468576
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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