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- PDB-6pdo: Human PIM1 bound to benzothiophene inhibitor 354 -

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Basic information

Entry
Database: PDB / ID: 6pdo
TitleHuman PIM1 bound to benzothiophene inhibitor 354
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 / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / 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 / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of 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 / Protein kinase, ATP binding site ...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-OD1 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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: Human PIM1
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 19, 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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5433
Polymers37,1832
Non-polymers3591
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint3 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.034, 96.034, 79.859
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-OD1 / 4-{5-[(3-aminopropyl)carbamoyl]thiophen-2-yl}-1-benzothiophene-2-carboxamide


Mass: 359.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.1 M HEPES pH7.5, 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: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.4→19.97 Å / Num. obs: 16433 / % possible obs: 99.8 % / Redundancy: 20.4 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.022 / Rrim(I) all: 0.101 / Net I/σ(I): 21 / Num. measured all: 334637
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 20.7 % / Rmerge(I) obs: 1.303 / Num. measured all: 35321 / Num. unique obs: 1709 / CC1/2: 0.93 / Rpim(I) all: 0.293 / Rrim(I) all: 1.336 / Net I/σ(I) obs: 2.6 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.25 Å19.97 Å
Translation3.25 Å19.97 Å

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Processing

Software
NameVersionClassification
XDS20190315data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.97 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 16.163 / SU ML: 0.176 / SU R Cruickshank DPI: 0.2571 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.209
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.223 725 4.4 %RANDOM
Rwork0.1753 ---
obs0.1774 15682 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 129.12 Å2 / Biso mean: 66.072 Å2 / Biso min: 44.14 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å21.13 Å20 Å2
2--2.27 Å2-0 Å2
3----7.36 Å2
Refinement stepCycle: final / Resolution: 2.4→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 24 54 2310
Biso mean--96.31 60.7 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132325
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172128
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.6393156
X-RAY DIFFRACTIONr_angle_other_deg1.1381.5784903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1295274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.28420.347144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83415381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9771524
X-RAY DIFFRACTIONr_chiral_restr0.0520.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02544
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 43 -
Rwork0.305 1155 -
all-1198 -
obs--99.92 %
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)
11.11530.6053-0.39563.41760.55170.69230.1995-0.0319-0.14780.0238-0.21210.15660.1127-0.18350.01260.1546-0.0775-0.08880.10350.03090.0659-22.4828.9968.159
20.3909-0.41730.50512.0361-0.43311.87150.1735-0.06310.00180.1235-0.19140.1448-0.0335-0.1480.01790.1985-0.06960.02720.14420.00950.0272-19.27233.71511.048
30.6719-0.0032-0.04850.7105-0.18661.06780.0332-0.0016-0.0194-0.06340.02750.01480.01540.023-0.06070.04790.014-0.01440.0702-0.00610.0078-2.81443.73-1.731
42.53531.6367-1.09341.3744-1.02383.5770.08670.62710.1018-0.13170.29620.01831.0228-0.8126-0.38290.3914-0.1175-0.08710.3470.12630.0724-8.24735.284-13.473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 89
2X-RAY DIFFRACTION2A90 - 124
3X-RAY DIFFRACTION3A125 - 305
4X-RAY DIFFRACTION4B2 - 9

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