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- PDB-7z6u: Pim1 in complex with (E)-4-((6-amino-2-oxoindolin-3-ylidene)methy... -

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Basic information

Entry
Database: PDB / ID: 7z6u
TitlePim1 in complex with (E)-4-((6-amino-2-oxoindolin-3-ylidene)methyl)benzoic acid and Pimtide
Components
  • Isoform 1 of Serine/threonine-protein kinase pim-1
  • Pimtide
KeywordsTRANSFERASE / SERINE KINASE / KINASE / COMPLEX / PIM1 / PIM / PIM-1 / INHIBITOR / TUMORIGENISIS / CANCER / PIMTIDE / PROTO ONCOGEN / ATP / PHOSPHORYLATION / APOPTOSIS / CELL CYCLE
Function / homologynon-specific serine/threonine protein kinase / Chem-IJB / Isoform 1 of Serine/threonine-protein kinase pim-1
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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
DepositionMar 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 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

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Assembly

Deposited unit
A: Isoform 1 of Serine/threonine-protein kinase pim-1
D: Pimtide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6784
Polymers37,3052
Non-polymers3722
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint3 kcal/mol
Surface area12610 Å2
Unit cell
Length a, b, c (Å)97.797, 97.797, 80.067
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 Isoform 1 of Serine/threonine-protein kinase pim-1


Mass: 35712.578 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: P11309-1, 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-IJB / 4-[(~{E})-(6-azanyl-2-oxidanylidene-1~{H}-indol-3-ylidene)methyl]benzoic acid


Mass: 280.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: May 29, 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: 2.28→48.899 Å / Num. obs: 19985 / % possible obs: 99.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 42.56 Å2 / CC1/2: 1 / Rsym value: 0.059 / Net I/σ(I): 27.9
Reflection shellResolution: 2.28→2.41 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 5.28 / Num. unique obs: 3159 / CC1/2: 1 / Rsym value: 0.46 / % possible all: 98.9

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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: 2.28→36.19 Å / SU ML: 0.2638 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.9585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1908 999 5 %
Rwork0.1617 18979 -
obs0.1632 19978 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.77 Å2
Refinement stepCycle: LAST / Resolution: 2.28→36.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 27 94 2296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762265
X-RAY DIFFRACTIONf_angle_d0.80473074
X-RAY DIFFRACTIONf_chiral_restr0.0515330
X-RAY DIFFRACTIONf_plane_restr0.0053417
X-RAY DIFFRACTIONf_dihedral_angle_d20.53641333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.40.23481400.17482661X-RAY DIFFRACTION98.84
2.4-2.550.22641420.17192683X-RAY DIFFRACTION99.93
2.55-2.740.22631430.17432723X-RAY DIFFRACTION99.93
2.74-3.020.20471420.16472701X-RAY DIFFRACTION99.96
3.02-3.460.20591430.16272720X-RAY DIFFRACTION100
3.46-4.350.16761440.14862729X-RAY DIFFRACTION99.97
4.35-36.190.17581450.16442762X-RAY DIFFRACTION99.83
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)
10.04127738553720.001418849660980.006113586287850.01748649066940.006376459264320.0100427692166-0.05375745827650.355410883253-0.222141850243-0.3479837612760.1349060895570.2616749618830.126326225097-0.1450314870540.0008445603835910.4317987156340.00345800842649-0.09136022402370.5532928973880.02838369601430.53100552879124.690624013194.172832334-16.4801526879
21.114214714880.1443663748760.1413587646870.4012808296180.1962604767550.100212064782-0.243647800099-0.0306823743430.541275683607-0.464608106425-0.5965622628110.133947585272-0.0763880665107-0.060750876204-0.2188665812820.7951685774190.3530130301350.07158272370950.7978359138-0.03699186467210.587363094931110.833963641209.754845362-0.588066836725
30.550442657601-0.18778637075-0.1425151708870.187662877325-0.1072307347210.233626782807-0.0570920044139-0.613524295923-0.1732621520920.00453532103610.09869002179940.343098557939-0.109003480002-0.4068238990990.0216209235560.4674008239680.0829981768610.04656708659130.4259328944520.0007919999999690.467468326755114.336393849201.1619782095.53920981018
40.705099340726-0.2909757488340.4794671103090.2448032480160.03803322128450.7468521674570.1478310026290.109814067140.601258105764-0.145161708010.1109881879620.1609889283-0.520362446842-0.329646137160.01780791283960.4211812842120.06396238026560.01782253617920.3877739285190.01128187987010.397281185223122.229538502204.880660002-0.780757420621
51.0975117239-0.209628694101-0.2175135376330.739599383429-0.3343851331282.249622678910.03168696238140.0876428249715-0.0524674740137-0.0239856742550.009440069668540.02385105455060.1293755702290.177784086119-1.53933275996E-50.3505908132170.0155165519602-0.01677819904420.295636512314-0.02402055863530.337444382869135.475486996192.879836738-4.66868542887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 2 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 140 )
5X-RAY DIFFRACTION5chain 'A' and (resid 141 through 305 )

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