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- PDB-8r0h: Pim1 in complex with (E)-3-(2-(thiophen-2-yl)vinyl)-3,4-dihydroqu... -

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Basic information

Entry
Database: PDB / ID: 8r0h
TitlePim1 in complex with (E)-3-(2-(thiophen-2-yl)vinyl)-3,4-dihydroquinoxalin-2(1H)-one 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 / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / 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 / Signaling by FLT3 fusion proteins ...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 / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / positive regulation of TORC1 signaling / negative regulation of innate immune response / 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 / 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 / : / 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
3-(2-thiophen-2-ylethenyl)-1~{H}-quinoxalin-2-one / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsHochban, P.M.M. / Heine, A. / Diederich, W.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Pim1 in complex with (E)-3-(2-(thiophen-2-yl)vinyl)-3,4-dihydroquinoxalin-2(1H)-one and Pimtide
Authors: Hochban, P.M.M. / Heyder, L. / Heine, A. / Diederich, W.E.
History
DepositionOct 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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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
B: Pimtide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7025
Polymers37,2632
Non-polymers4383
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint3 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.304, 98.304, 80.339
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 / 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.) Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-8UB / 3-(2-thiophen-2-ylethenyl)-1~{H}-quinoxalin-2-one


Mass: 254.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10N2OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.06 Å3/Da / Density % sol: 59.83 %
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: Feb 1, 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: 1.88→49.15 Å / Num. obs: 35994 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 27.11 Å2 / CC1/2: 0.99 / Rsym value: 7 / Net I/σ(I): 17.7
Reflection shellResolution: 1.88→1.89 Å / Num. unique obs: 5758 / CC1/2: 0.92 / Rsym value: 52.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEdata collection
XDS1.02data reduction
XDS1.02data scaling
PHASERphasing
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→49.15 Å / SU ML: 0.162 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.8345
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1741 1800 5 %
Rwork0.1544 34189 -
obs0.1554 35989 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.72 Å2
Refinement stepCycle: LAST / Resolution: 1.88→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 30 207 2490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712405
X-RAY DIFFRACTIONf_angle_d0.8033269
X-RAY DIFFRACTIONf_chiral_restr0.0524347
X-RAY DIFFRACTIONf_plane_restr0.0083444
X-RAY DIFFRACTIONf_dihedral_angle_d11.6132896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.23331380.20182618X-RAY DIFFRACTION98.82
1.93-1.990.19871380.16912622X-RAY DIFFRACTION100
1.99-2.050.21011370.15392618X-RAY DIFFRACTION99.96
2.05-2.120.18511370.15712593X-RAY DIFFRACTION100
2.12-2.210.18541380.15092614X-RAY DIFFRACTION99.96
2.21-2.310.17321390.14622647X-RAY DIFFRACTION100
2.31-2.430.17071380.14582623X-RAY DIFFRACTION99.96
2.43-2.580.19171380.16462629X-RAY DIFFRACTION99.93
2.58-2.780.19731380.17112621X-RAY DIFFRACTION99.96
2.78-3.060.17691390.15662637X-RAY DIFFRACTION99.96
3.06-3.510.16951380.15452627X-RAY DIFFRACTION99.89
3.51-4.410.14891400.13442650X-RAY DIFFRACTION100
4.42-49.150.16571420.16082690X-RAY DIFFRACTION99.68
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)
10.3603450119940.1696007814930.1617697932210.2095952750810.2977519187030.455976984511-0.07640466643540.4124025517540.03081835635220.09420799030740.2163304266770.239279549256-0.213694906063-0.4076979666930.008573631232840.3915759942610.06569629781880.02078333403220.3060501884840.0632885815220.306866296333133.683169632-11.0343430996-12.6693964936
20.2925022714170.0160733178442-0.3316688583010.219540103765-0.2642564735631.34261529442-0.0230950483270.05491984817320.407732685589-0.05006912398660.0612161359943-0.0369260481653-0.492876981388-0.1710372780150.1248085168940.427401608026-0.03265713658030.0312599630550.183789412777-0.01260600428080.35563296522138.8881516296.887296502964.9355910438
30.02804494351960.01760167909590.02010159645040.07503769398350.03602091059040.03782171006160.0696702132219-0.237270939095-0.08895947555080.3480770272850.1685763059990.115762590799-0.0942688379944-0.154172426252-0.0003780505574740.3585336395750.03769999294740.1136550285630.2601202828490.02075421504410.285846893563127.92784177-3.8618812114814.1538736719
40.217886931973-0.2091938621040.2656320122480.485399280275-0.2765192544540.5157983204590.0224022535031-0.0007659053629320.238570575289-0.03377199333030.138469483701-0.164244973848-0.3901356396120.1224919684610.01862795583680.311891061138-0.03151498481430.02122536217930.199450546047-0.0009051739126450.264401818787141.74227462-3.627806572533.19815958827
50.778011416085-0.156589654337-0.07007797804710.8235449350730.02177465200181.694534261920.05708322578610.0287284511397-0.03053951751460.0458063833851-0.02345229561350.0132409981460.0735887109615-0.0485602697846-1.73606826319E-50.181947946486-0.025023448711-0.005315079175040.1795134040010.01312351621040.192734630733137.56714478-21.0701964922-0.936316284836
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 2 through 10 )BC2 - 101 - 9
22chain 'A' and (resid 33 through 73 )AA33 - 731 - 41
33chain 'A' and (resid 74 through 96 )AA74 - 9642 - 64
44chain 'A' and (resid 97 through 140 )AA97 - 14065 - 108
55chain 'A' and (resid 141 through 305 )AA141 - 305109 - 273

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