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

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Basic information

Entry
Database: PDB / ID: 5vub
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 / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / 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 / 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 / transcription factor binding / ribosomal small subunit 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 / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / 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 / 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-8GU / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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

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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)34,6863
Polymers34,2041
Non-polymers4832
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.100, 98.100, 80.610
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: 34203.727 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-8GU / (2Z)-6-methoxy-7-(piperazin-1-ylmethyl)-2-(1H-pyrrolo[3,2-b]pyridin-3-ylmethylidene)-1-benzofuran-3-one


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


Mass: 18.015 Da / Num. of mol.: 235 / 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→31.144 Å / Num. obs: 29862 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 27.55 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Rsym value: 0.068 / Net I/av σ(I): 7.6 / Net I/σ(I): 18.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2-2.116.40.4391.70.1880.4770.439100
2.11-2.246.40.2932.60.1250.3190.293100
2.24-2.396.40.1794.20.0760.1950.179100
2.39-2.586.40.1295.90.0550.140.129100
2.58-2.836.40.098.30.0380.0980.09100
2.83-3.166.40.0696.60.0290.0750.069100
3.16-3.656.40.0639.20.0270.0680.063100
3.65-4.476.40.04612.10.020.050.04699.9
4.47-6.326.40.03117.30.0130.0330.03199.9
6.32-32.1116.20.02324.40.010.0250.02398.7

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Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALA3.2.25data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→31.14 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.29
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 1482 4.97 %Transferred from model
Rwork0.1603 ---
obs0.1614 29846 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.92 Å2 / Biso mean: 32.39 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 2→31.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 35 238 2470
Biso mean--31.22 39.53 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052330
X-RAY DIFFRACTIONf_angle_d0.9323170
X-RAY DIFFRACTIONf_chiral_restr0.067333
X-RAY DIFFRACTIONf_plane_restr0.004410
X-RAY DIFFRACTIONf_dihedral_angle_d17.938874
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0001-2.06470.22621370.187525522689
2.0647-2.13840.19081310.17125892720
2.1384-2.2240.18251410.16725472688
2.224-2.32520.17321250.158125802705
2.3252-2.44780.18831330.165625912724
2.4478-2.60110.2141440.16825452689
2.6011-2.80180.19611210.175325942715
2.8018-3.08350.19361400.167425722712
3.0835-3.52920.20761460.159825702716
3.5292-4.44430.15661320.137725862718
4.4443-31.14420.1631320.161626382770
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)
13.80570.34391.05122.7436-0.65433.8903-0.0569-0.2135-0.7245-0.11020.1086-0.16520.3751-0.3518-0.03630.3565-0.0197-0.01430.13070.04980.35640.3588-6.2957-3.1357
29.11294.294-1.78646.3776-3.76397.81760.24760.9493-0.325-0.43630.52350.70170.0089-1.0547-0.63790.57230.0834-0.17530.33930.01920.378229.70073.8558-13.7099
32.41652.02211.18474.46191.98172.5475-0.02730.0332-0.3258-0.16680.2098-0.21010.29430.1061-0.15670.23470.0385-0.00180.16050.04190.203343.61793.6395-2.4534
41.88710.09160.65652.01220.4662.78240.0202-0.1153-0.0135-0.0864-0.00370.0672-0.0606-0.0808-0.00670.14090.02150.00920.10820.03170.108839.3421.24361.8431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 36 through 73 )B36 - 73
2X-RAY DIFFRACTION2chain 'B' and (resid 74 through 96 )B74 - 96
3X-RAY DIFFRACTION3chain 'B' and (resid 97 through 140 )B97 - 140
4X-RAY DIFFRACTION4chain 'B' and (resid 141 through 305 )B141 - 305

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