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- PDB-9krz: Crystal structure Of MerTK kinase domain in complex with compound 11 -

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Basic information

Entry
Database: PDB / ID: 9krz
TitleCrystal structure Of MerTK kinase domain in complex with compound 11
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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / 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: 2.6 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)69,0304
Polymers67,7122
Non-polymers1,3172
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-13 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.577, 91.427, 68.947
Angle α, β, γ (deg.)90.00, 100.38, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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-A1L6K / ~{N}-[4-[5-[3-[(dimethylamino)methyl]phenyl]-6-(1-methylpyrazol-4-yl)furo[2,3-d]pyrimidin-4-yl]oxyphenyl]-2-(4-fluorophenyl)-1-methyl-3-oxidanylidene-pyrazole-4-carboxamide


Mass: 658.681 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H31FN8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
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 15, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 18871 / % possible obs: 98.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 47.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.7
Reflection shellResolution: 2.62→2.71 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 1729 / CC1/2: 0.843

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Processing

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

3tcp


Resolution: 2.6→28.79 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 870 4.68 %
Rwork0.2213 --
obs0.2235 18582 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 0 20 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.635
X-RAY DIFFRACTIONf_dihedral_angle_d9.322574
X-RAY DIFFRACTIONf_chiral_restr0.04651
X-RAY DIFFRACTIONf_plane_restr0.005718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.37641360.29912632X-RAY DIFFRACTION87
2.76-2.980.31441510.25612986X-RAY DIFFRACTION99
2.98-3.280.3071520.25232995X-RAY DIFFRACTION100
3.28-3.750.29711350.20913021X-RAY DIFFRACTION100
3.75-4.720.23171410.18893025X-RAY DIFFRACTION99
4.72-5.630.23191550.21943053X-RAY DIFFRACTION99

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