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- PDB-7akg: Crystal structure of STK17B with bound dovitinib -

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Basic information

Entry
Database: PDB / ID: 7akg
TitleCrystal structure of STK17B with bound dovitinib
ComponentsSerine/threonine-protein kinase 17B
KeywordsTRANSFERASE / kinase / STK17B / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation ...positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleoplasm / ATP binding / nucleus / plasma membrane
Similarity search - Function
Serine/threonine-protein kinase 17B, catalytic domain / 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
Chem-38O / Serine/threonine-protein kinase 17B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsChaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2020
Title: A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation.
Authors: Picado, A. / Chaikuad, A. / Wells, C.I. / Shrestha, S. / Zuercher, W.J. / Pickett, J.E. / Kwarcinski, F.E. / Sinha, P. / de Silva, C.S. / Zutshi, R. / Liu, S. / Kannan, N. / Knapp, S. / ...Authors: Picado, A. / Chaikuad, A. / Wells, C.I. / Shrestha, S. / Zuercher, W.J. / Pickett, J.E. / Kwarcinski, F.E. / Sinha, P. / de Silva, C.S. / Zutshi, R. / Liu, S. / Kannan, N. / Knapp, S. / Drewry, D.H. / Willson, T.M.
History
DepositionSep 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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 17B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0307
Polymers37,3271
Non-polymers7036
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint11 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.289, 84.289, 114.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

21A-571-

HOH

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Components

#1: Protein Serine/threonine-protein kinase 17B / DAP kinase-related apoptosis-inducing protein kinase 2


Mass: 37327.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK17B, DRAK2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: O94768, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-38O / 4-amino-5-fluoro-3-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]quinolin-2(1H)-one / Dovitinib


Mass: 392.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21FN6O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 10% PEG 3350, 0.2M NaCl and 0.1M bis-tris pH 5.5

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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 PILATUS3 6M / Detector: PIXEL / Date: Sep 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.08→47.27 Å / Num. obs: 25428 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.04 / Rrim(I) all: 0.128 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.08-2.148.40.8492.319360.4740.3290.964100
9.07-47.277.70.0623800.9880.0250.06899.4

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LM0

3lm0


Resolution: 2.08→47.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / SU B: 9.149 / SU ML: 0.125 / SU R Cruickshank DPI: 0.1719 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1195 4.7 %RANDOM
Rwork0.1856 ---
obs0.1872 24201 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.03 Å2 / Biso mean: 47.402 Å2 / Biso min: 21.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å20 Å2
2--0.59 Å20 Å2
3----1.18 Å2
Refinement stepCycle: final / Resolution: 2.08→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 49 193 2594
Biso mean--53.59 48.39 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192488
X-RAY DIFFRACTIONr_bond_other_d0.0020.022271
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9613378
X-RAY DIFFRACTIONr_angle_other_deg0.87235297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34225.372121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34615435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7041510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022865
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02481
LS refinement shellResolution: 2.08→2.134 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 77 -
Rwork0.306 1751 -
all-1828 -
obs--99.95 %
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)
10.0785-0.1364-0.02881.02050.54540.3729-0.0009-0.03570.0159-0.01770.00810.07220.0071-0.0028-0.00710.0319-0.00770.0180.0457-0.02770.329926.6612.7783.917
21.98240.2006-0.29530.841-0.47081.3765-0.08730.4913-0.0265-0.0390.0685-0.0938-0.0132-0.05070.01880.008-0.02140.00710.1266-0.01660.330419.0124.1438.022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 183
2X-RAY DIFFRACTION2A184 - 309

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