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- PDB-5vua: Pim1 Kinase in complex with a benzofuranone inhibitor -

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Basic information

Entry
Database: PDB / ID: 5vua
TitlePim1 Kinase in complex with a benzofuranone inhibitor
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / Pim1 kinase / kinase inhibitor
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 / positive regulation of brown fat cell differentiation / Signaling by FLT3 fusion proteins / 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-8GX / PHOSPHATE ION / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsParker, L.J.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHIJP15582248 Japan
CitationJournal: J Chem Inf Model / Year: 2017
Title: Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach
Authors: Watanabe, C. / Watanabe, H. / Fukuzawa, K. / Parker, L.J. / Okiyama, Y. / Yuki, H. / Yokoyama, S. / Nakano, H. / Tanaka, S. / Honma, T.
History
DepositionMay 18, 2017Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 20, 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
B: Serine/threonine-protein kinase pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7654
Polymers34,1881
Non-polymers5773
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-3 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.140, 98.140, 80.510
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: 34187.727 Da / Num. of mol.: 1 / Fragment: UNP residues 120-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1
Production host: Cell-free gateway cloning vector C-term 8xHis pCellFree_G02 (others)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-8GX / (2Z)-6-methoxy-7-(piperazin-1-ylmethyl)-2-(1H-pyrrolo[2,3-c]pyridin-3-ylmethylidene)-1-benzofuran-3-one


Mass: 390.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100MM CITRATE BUFFER, PH 5.5, 200MM NACL, 1M NH4HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→32.125 Å / Num. all: 22490 / Num. obs: 22490 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.42 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Rsym value: 0.077 / Net I/av σ(I): 7 / Net I/σ(I): 17.3 / Num. measured all: 143178
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.326.40.3822077132630.1640.4140.385.5100
2.32-2.466.40.2692.81971830990.1160.2930.2697.6100
2.46-2.636.40.1993.81856029030.0850.2170.1999.6100
2.63-2.846.40.1365.51724226960.0590.1480.13612.7100
2.84-3.116.40.0927.81607625120.0390.10.09217.6100
3.11-3.486.40.0881445922640.0340.0870.0823.1100
3.48-4.026.40.0727.61274319940.0310.0780.07228.8100
4.02-4.926.40.05211.21084817050.0220.0570.05233.3100
4.92-6.966.30.02720.5829613100.0120.030.02735.8100
6.96-32.12560.01929.844657440.0090.0210.01937.299.1

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
MOSFLMdata collection
SCALA3.2.25data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.124 Å / FOM work R set: 0.8812 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1122 4.99 %transferred from model
Rwork0.1655 21341 --
obs0.1671 22463 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.34 Å2 / Biso mean: 35.24 Å2 / Biso min: 14.68 Å2
Refinement stepCycle: final / Resolution: 2.2→32.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 40 216 2446
Biso mean--35.57 41.6 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052317
X-RAY DIFFRACTIONf_angle_d0.8613154
X-RAY DIFFRACTIONf_chiral_restr0.063333
X-RAY DIFFRACTIONf_plane_restr0.004406
X-RAY DIFFRACTIONf_dihedral_angle_d15.017862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.30010.24291460.202726652811
2.3001-2.42130.2251340.177926352769
2.4213-2.5730.23951450.180826632808
2.573-2.77150.21211240.179626702794
2.7715-3.05030.21991520.168526412793
3.0503-3.49120.2041490.166826672816
3.4912-4.39670.16161390.14126722811
4.3967-32.12720.17331330.165327282861

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