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- PDB-7oam: Kinase domain of MERTK in complex with compound 8 -

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Basic information

Entry
Database: PDB / ID: 7oam
TitleKinase domain of MERTK in complex with compound 8
ComponentsTyrosine-protein kinase Mer
KeywordsTRANSFERASE / MERTK / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
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 / positive regulation of 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 / phagocytosis / positive regulation of phagocytosis / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / establishment of localization in cell / Cell surface interactions at the vascular wall / receptor protein-tyrosine kinase / platelet activation / cell migration / cell-cell signaling / retina development in camera-type eye / nervous system development / spermatogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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-V6H / Tyrosine-protein kinase Mer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSchroeder, M. / Russ, N. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2021
Title: Design and Development of a Chemical Probe for Pseudokinase Ca 2+ /calmodulin-Dependent Ser/Thr Kinase.
Authors: Russ, N. / Schroder, M. / Berger, B.T. / Mandel, S. / Aydogan, Y. / Mauer, S. / Pohl, C. / Drewry, D.H. / Chaikuad, A. / Muller, S. / Knapp, S.
History
DepositionApr 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)68,8086
Polymers68,1492
Non-polymers6594
Water86548
1
A: Tyrosine-protein kinase Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1993
Polymers34,0751
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein kinase Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6093
Polymers34,0751
Non-polymers5352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.487, 91.315, 69.680
Angle α, β, γ (deg.)90.000, 100.780, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Label seq-ID: 8 - 294

Dom-IDAuth asym-IDLabel asym-IDAuth seq-ID
1AA576 - 861
2BB576 - 862

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Components

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


Mass: 34074.504 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-V6H / 2-[[2,5-bis(fluoranyl)phenyl]methylamino]-4-(cyclopentylamino)-N-[3-(2-oxidanylidenepyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide


Mass: 472.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30F2N6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 35% PEG 400, 0.2M MgCl2, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→45.66 Å / Num. obs: 18384 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.079 / Rrim(I) all: 0.194 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.65-2.785.91.0551438724510.6730.4691.1581.899.4
8.79-45.6660.0931945280.9890.040.09813.399.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m3q

4m3q


Resolution: 2.65→45.66 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.903 / SU B: 25.763 / SU ML: 0.258 / SU R Cruickshank DPI: 0.9717 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.972 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 903 4.9 %RANDOM
Rwork0.2218 ---
obs0.2235 17465 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.34 Å2 / Biso mean: 49.289 Å2 / Biso min: 14.52 Å2
Baniso -1Baniso -2Baniso -3
1-3.3 Å2-0 Å20.32 Å2
2---1.68 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: final / Resolution: 2.65→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3893 0 46 48 3987
Biso mean--66.34 46.01 -
Num. residues----510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134020
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173796
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.6365458
X-RAY DIFFRACTIONr_angle_other_deg1.1671.5878706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7095502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77522.012169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61815652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5261520
X-RAY DIFFRACTIONr_chiral_restr0.0540.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02852
Refine LS restraints NCS

Ens-ID: 1 / Number: 7093 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 73 -
Rwork0.292 1309 -
all-1382 -
obs--99.28 %
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)
13.551-1.6582.24490.8827-1.42453.06870.09570.29230.046-0.0558-0.07020.0651-0.0198-0.1235-0.02540.2329-0.0469-0.06410.21280.04190.2713-18.233-25.62810.564
21.69010.4469-0.74282.851-0.56522.47050.0901-0.07550.05440.0042-0.0010.1972-0.0017-0.0509-0.08910.07850.0225-0.01760.0178-0.00940.0392-1.544-7.6185.126
33.4454-0.18261.15342.5081-0.36761.7474-0.064-0.3265-0.02090.18240.0950.4451-0.1396-0.6818-0.03110.21270.0456-0.0060.2730.00390.1105-17.75231.74516.938
41.48990.03130.08483.8010.073.7425-0.0784-0.01980.00690.07750.01850.01020.0525-0.03490.060.07290.0295-0.00820.0202-0.02360.0534-5.18910.66830.285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A575 - 643
2X-RAY DIFFRACTION2A644 - 862
3X-RAY DIFFRACTION3B576 - 673
4X-RAY DIFFRACTION4B674 - 862

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