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- PDB-7m5z: Crystal Structure of the MerTK Kinase Domain in Complex with Inhi... -

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Basic information

Entry
Database: PDB / ID: 7m5z
TitleCrystal Structure of the MerTK Kinase Domain in Complex with Inhibitor MIPS15692
ComponentsTyrosine-protein kinase Mer
KeywordsSIGNALING PROTEIN/INHIBITOR / Kinase / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / positive regulation of phagocytosis / phagocytosis ...negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / positive regulation of phagocytosis / phagocytosis / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / phosphatidylinositol 3-kinase/protein kinase B signal transduction / establishment of localization in cell / Cell surface interactions at the vascular wall / receptor protein-tyrosine kinase / platelet activation / cell surface receptor protein tyrosine kinase signaling pathway / cell migration / retina development in camera-type eye / cell-cell signaling / nervous system development / spermatogenesis / cell surface receptor signaling pathway / receptor complex / protein phosphorylation / extracellular space / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-YR7 / Tyrosine-protein kinase Mer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsHermans, S.J. / Hancock, N.C. / Baell, J.B. / Parker, M.W.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Development of [ 18 F]MIPS15692, a radiotracer with in vitro proof-of-concept for the imaging of MER tyrosine kinase (MERTK) in neuroinflammatory disease.
Authors: Wong, S.W. / Vivash, L. / Mudududdla, R. / Nguyen, N. / Hermans, S.J. / Shackleford, D.M. / Field, J. / Xue, L. / Aprico, A. / Hancock, N.C. / Haskali, M. / Stashko, M.A. / Frye, S.V. / ...Authors: Wong, S.W. / Vivash, L. / Mudududdla, R. / Nguyen, N. / Hermans, S.J. / Shackleford, D.M. / Field, J. / Xue, L. / Aprico, A. / Hancock, N.C. / Haskali, M. / Stashko, M.A. / Frye, S.V. / Wang, X. / Binder, M.D. / Ackermann, U. / Parker, M.W. / Kilpatrick, T.J. / Baell, J.B.
History
DepositionMar 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Mer
B: Tyrosine-protein kinase Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9044
Polymers72,0032
Non-polymers9012
Water1629
1
A: Tyrosine-protein kinase Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4522
Polymers36,0011
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4522
Polymers36,0011
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.203, 91.272, 100.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein kinase Mer / Proto-oncogene c-Mer / Receptor tyrosine kinase MerTK


Mass: 36001.488 Da / Num. of mol.: 2 / Fragment: Kinase Domain, UNP residues 570-864
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MERTK, MER / Production host: Escherichia coli (E. coli)
References: UniProt: Q12866, receptor protein-tyrosine kinase
#2: Chemical ChemComp-YR7 / 2-(butylamino)-N-[1-(3-fluoropropyl)piperidin-4-yl]-4-{[(1r,4r)-4-hydroxycyclohexyl]amino}pyrimidine-5-carboxamide


Mass: 450.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H39FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Bis-tris Propane pH 7.5, 2.2 M Sodium Chloride, and 0.15 M Magnesium Chloride
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953731894493 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731894493 Å / Relative weight: 1
ReflectionResolution: 3.06→48.72 Å / Num. obs: 11670 / % possible obs: 91.4 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.055 / Rrim(I) all: 0.141 / Net I/σ(I): 9.2
Reflection shellResolution: 3.06→3.27 Å / Redundancy: 7 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2255 / CC1/2: 0.911 / Rpim(I) all: 0.292 / Rrim(I) all: 0.773 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ab0

7ab0


Resolution: 3.06→44.122 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2974 565 4.89 %
Rwork0.2627 --
obs0.2646 11559 90.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.06→44.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 64 9 4327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034423
X-RAY DIFFRACTIONf_angle_d0.7055975
X-RAY DIFFRACTIONf_dihedral_angle_d11.2593750
X-RAY DIFFRACTIONf_chiral_restr0.042663
X-RAY DIFFRACTIONf_plane_restr0.005753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.36790.41511390.33262959X-RAY DIFFRACTION100
3.3679-3.85490.33511180.2882179X-RAY DIFFRACTION73
3.8549-4.85590.28541550.23362721X-RAY DIFFRACTION91

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