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- PDB-8r27: Pim1 in complex with (Z)-4-(1-cyano-2-(4-hydroxyphenyl)vinyl)benz... -

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Basic information

Entry
Database: PDB / ID: 8r27
TitlePim1 in complex with (Z)-4-(1-cyano-2-(4-hydroxyphenyl)vinyl)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 / 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 / protein serine/threonine kinase activator activity / negative regulation of innate immune response / 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
: / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 (Z)-4-(1-cyano-2-(4-hydroxyphenyl)vinyl)benzoic acid and Pimtide
Authors: Hochban, P.M.M. / Heyder, L. / Heine, A. / Diederich, W.E.
History
DepositionNov 3, 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)37,5434
Polymers37,2632
Non-polymers2792
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint3 kcal/mol
Surface area12740 Å2
Unit cell
Length a, b, c (Å)97.085, 97.085, 80.116
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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-XJW / 4-[(~{Z})-1-cyanoprop-1-enyl]benzoic acid


Mass: 187.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 59.9 %
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: Oct 23, 2020
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→48.54 Å / Num. obs: 30949 / % possible obs: 98.7 % / Redundancy: 20.8 % / Biso Wilson estimate: 39.59 Å2 / CC1/2: 0.99 / Net I/σ(I): 25.2
Reflection shellResolution: 1.95→1.96 Å / Num. unique obs: 4915 / CC1/2: 0.87

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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: 1.95→48.54 Å / SU ML: 0.1974 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3059
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.192 1548 5 %
Rwork0.1645 29396 -
obs0.1658 30944 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.93 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 20 112 2344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722309
X-RAY DIFFRACTIONf_angle_d0.77973134
X-RAY DIFFRACTIONf_chiral_restr0.0552335
X-RAY DIFFRACTIONf_plane_restr0.0099413
X-RAY DIFFRACTIONf_dihedral_angle_d26.212836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.28581380.23662612X-RAY DIFFRACTION96.9
2.01-2.080.23911380.1892632X-RAY DIFFRACTION98.3
2.08-2.170.19591410.17772671X-RAY DIFFRACTION98.42
2.17-2.270.19471390.16472642X-RAY DIFFRACTION98.83
2.27-2.390.17631410.15232681X-RAY DIFFRACTION99.05
2.39-2.540.22531410.1642677X-RAY DIFFRACTION99.16
2.54-2.730.21161390.17172650X-RAY DIFFRACTION97.79
2.73-3.010.18471420.16712692X-RAY DIFFRACTION99.4
3.01-3.440.21171420.16312702X-RAY DIFFRACTION99.65
3.44-4.330.14831420.15262701X-RAY DIFFRACTION98.96
4.34-48.540.20271450.16562736X-RAY DIFFRACTION98.97
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)
11.79384309264-0.291287809347-0.3731029762491.38909814662-0.5817282434182.833525091770.0158912262869-0.07846389198230.04380434297750.129009356020.0782063929239-0.0231853043320.1151504185690.134148445735-2.52049247499E-60.265851279508-0.010361715534-0.000112930447490.345694031241-0.03005140053780.30779017917447.1882942486-127.9516334010.215916267009
20.575967274870.3894300167370.03239592081630.296681098079-0.07663727525050.2977131396070.478076283813-0.6907344813080.2000555827550.584946448244-0.175629661668-0.240573182425-0.5979485309330.406552341407-0.01453854005890.5611968806310.1053878416730.07600481906660.561542391799-0.07530801126470.49053996337840.5718950703-119.84301656512.7082932785
30.3271654526030.7831180026880.1061801685911.878317073640.2563361333130.03506622607670.0765599775948-0.2611221201460.1651811536530.740778287854-0.434209143823-0.03033450682850.1766501929040.290564209173-0.08259522625910.566900665780.217215962058-0.008619665188910.882779134933-0.0857241438260.81452363970520.298775393-115.49699222-3.44908552562
40.466886867905-0.416845908388-0.08009862695070.477044855790.05472077201480.493268077630.4697396518250.3208930362240.352482210845-0.237611476287-0.4304456442360.0145425501596-0.390780747311-0.4496985703910.008378523115040.3576976009250.05424710901010.03462050755390.521781591620.03390453862250.47483717531129.297102945-113.703034407-10.284610227
50.840365328743-0.486652818528-0.2745899026750.8157509846060.912058752121.153377814630.0849587054796-0.179323815906-0.061084462692-0.1816764269720.08641489567890.3337257204430.129882541694-0.7359176372430.01050104361120.3332728643810.0007560811889290.02073387475080.4807941296670.01198679154830.38982781074629.9535606069-122.526641942-3.5985643646
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 141 through 305 )AA141 - 305108 - 272
22chain 'B' and (resid 2 through 9 )BC2 - 91 - 8
33chain 'A' and (resid 33 through 50 )AA33 - 501 - 18
44chain 'A' and (resid 51 through 96 )AA51 - 9619 - 63
55chain 'A' and (resid 97 through 140 )AA97 - 14064 - 107

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