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- PDB-9kry: Crystal structure Of MerTK kinase domain in complex With compound 1 -

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Basic information

Entry
Database: PDB / ID: 9kry
TitleCrystal structure Of MerTK kinase domain in complex With compound 1
ComponentsTyrosine-protein kinase Mer
KeywordsTRANSFERASE / kinase / dynamic dimer / Complex / TAM / Immune regulation / allosteric binding inhibitor / Type 2 inhibitor
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 / phagocytosis / transmembrane receptor protein tyrosine kinase activity ...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 / phagocytosis / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / cell surface receptor protein tyrosine kinase signaling pathway / Cell surface interactions at the vascular wall / establishment of localization in cell / receptor protein-tyrosine kinase / platelet activation / cell migration / nervous system development / cell-cell signaling / retina development in camera-type eye / spermatogenesis / cell surface receptor signaling pathway / protein phosphorylation / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 ...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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
: / Tyrosine-protein kinase Mer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPeng, Y.H. / Lee, L.C. / Hsueh, C.C. / Wu, S.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Structure-Based Design of Potent and Selective MerTK Inhibitors by Modulating the Conformation of alpha C Helix.
Authors: Peng, Y.H. / Li, M.C. / Yen, W.C. / Yeh, T.K. / Hsueh, C.C. / Kuo, F.M. / Lai, Y.L. / Chang, L. / Lee, L.C. / Chen, P.Y. / Yen, K.J. / Chang, T.Y. / Sun, H.Y. / Chang, C.Y. / Hsieh, S.H. / ...Authors: Peng, Y.H. / Li, M.C. / Yen, W.C. / Yeh, T.K. / Hsueh, C.C. / Kuo, F.M. / Lai, Y.L. / Chang, L. / Lee, L.C. / Chen, P.Y. / Yen, K.J. / Chang, T.Y. / Sun, H.Y. / Chang, C.Y. / Hsieh, S.H. / Yang, C.M. / Hsieh, H.P. / Wu, S.Y.
History
DepositionNov 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)68,9464
Polymers67,7122
Non-polymers1,2332
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-1 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.994, 91.279, 69.227
Angle α, β, γ (deg.)90.00, 100.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33856.230 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MERTK, MER / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
Variant (production host): BL21(DE3)pLysS Escherichia coli pLysS
References: UniProt: Q12866, receptor protein-tyrosine kinase
#2: Chemical ChemComp-A1L6J / ~{N}-[4-[5-(3-aminophenyl)-6-(1-methylpyrazol-4-yl)furo[2,3-d]pyrimidin-4-yl]oxyphenyl]-2-(4-fluorophenyl)-1-methyl-3-oxidanylidene-pyrazole-4-carboxamide


Mass: 616.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H25FN8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 36% PEG 200, 0.05 M Calcium chloride dehydrate, 0.1 M MES monohydrate pH 7.1
PH range: 6.1-7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 5, 2021
RadiationMonochromator: liquid-nitrogen-cooling Si double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 29225 / % possible obs: 98.5 % / Redundancy: 5.2 % / CC1/2: 0.997 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.25-2.334.30.59227340.850.9590.3070.6691.01491.8
2.33-2.424.70.5527890.8980.9730.2740.6161.01495.5
2.42-2.535.10.48929250.9340.9830.2330.5431.02398.8
2.53-2.675.50.39629820.9580.9890.1820.4371.053100
2.67-2.835.60.30529480.9770.9940.1380.3361.052100
2.83-3.055.60.20129320.9870.9970.0920.2221.05100
3.05-3.365.50.12429590.9940.9980.0580.1371.02100
3.36-3.855.40.07929800.9950.9990.0380.0881.05100
3.85-4.845.20.05929570.9960.9990.030.0661.06299.6
4.84-105.20.05330190.9970.9990.0270.061.07899.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TCP

3tcp


Resolution: 2.25→29.31 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 33.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2844 1466 5.02 %
Rwork0.2396 --
obs0.2418 29191 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 0 106 4097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.824
X-RAY DIFFRACTIONf_dihedral_angle_d7.198545
X-RAY DIFFRACTIONf_chiral_restr0.045620
X-RAY DIFFRACTIONf_plane_restr0.0071184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.330.40241510.30422583X-RAY DIFFRACTION92
2.33-2.420.35381450.29552645X-RAY DIFFRACTION95
2.42-2.530.36211360.27492780X-RAY DIFFRACTION99
2.53-2.670.31161640.27732816X-RAY DIFFRACTION100
2.67-2.830.32781540.26472790X-RAY DIFFRACTION100
2.83-3.050.32861510.25192780X-RAY DIFFRACTION100
3.05-3.360.29881400.25522817X-RAY DIFFRACTION100
3.36-3.840.2581490.21672825X-RAY DIFFRACTION100
3.85-4.840.23961390.20312813X-RAY DIFFRACTION100
4.84-100.25551370.23862876X-RAY DIFFRACTION100

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