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- PDB-6pcw: Human PIM1 bound to benzothiophene inhibitor 213 -

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Basic information

Entry
Database: PDB / ID: 6pcw
TitleHuman PIM1 bound to benzothiophene inhibitor 213
Components
  • Peptide
  • Serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1 / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
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 / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response ...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 / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / positive regulation of TORC1 signaling / 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 / non-specific serine/threonine protein kinase / protein stabilization / 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 / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase pim-1/2/3 / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-O97 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGodoi, P.H.C. / Santiago, A.S. / Fala, A.M. / Ramos, P.Z. / Sriranganadane, D. / Mascarello, A. / Segretti, N. / Azevedo, H. / Guimaraes, C.R.W. / Arruda, P. ...Godoi, P.H.C. / Santiago, A.S. / Fala, A.M. / Ramos, P.Z. / Sriranganadane, D. / Mascarello, A. / Segretti, N. / Azevedo, H. / Guimaraes, C.R.W. / Arruda, P. / Elkins, J.M. / Counago, R.M. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To Be Published
Title: PIM1 bound to benzothiophene inhibitor
Authors: Godoi, P.H.C. / Santiago, A.S. / Fala, A.M. / Ramos, P.Z. / Sriranganadane, D. / Mascarello, A. / Segretti, N. / Azevedo, H. / Guimaraes, C.R.W. / Arruda, P. / Elkins, J.M. / Counago, R.M.
History
DepositionJun 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase pim-1
B: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7105
Polymers37,1832
Non-polymers5273
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint3 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.921, 96.921, 80.092
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Serine/threonine-protein kinase pim-1


Mass: 35590.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Protein/peptide Peptide


Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-O97 / 4-[5-(cyclopropylcarbamoyl)thiophen-2-yl]-1-benzothiophene-2-carboxamide


Mass: 342.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG3350, 0.1 M TRIS pH8.5, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.2→31.72 Å / Num. obs: 21801 / % possible obs: 99.9 % / Redundancy: 20.4 % / CC1/2: 1 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.025 / Rrim(I) all: 0.111 / Net I/σ(I): 23.3 / Num. measured all: 444854
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 20.6 % / Rmerge(I) obs: 2.465 / Num. measured all: 38500 / Num. unique obs: 1867 / CC1/2: 0.828 / Rpim(I) all: 0.553 / Rrim(I) all: 2.526 / Net I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDS20190315data reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IJP

4ijp


Resolution: 2.2→31.72 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.897 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.172
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1118 5.1 %RANDOM
Rwork0.1742 ---
obs0.1768 20653 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 154.52 Å2 / Biso mean: 57.839 Å2 / Biso min: 37.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20.92 Å20 Å2
2--1.84 Å2-0 Å2
3----5.98 Å2
Refinement stepCycle: final / Resolution: 2.2→31.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 35 67 2376
Biso mean--93.78 52.64 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132370
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172159
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.6393214
X-RAY DIFFRACTIONr_angle_other_deg1.3031.5764981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.00120.483145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90515383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8671523
X-RAY DIFFRACTIONr_chiral_restr0.0670.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022661
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02548
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 83 -
Rwork0.318 1511 -
all-1594 -
obs--99.81 %

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