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- PDB-6mwe: CRYSTAL STRUCTURE OF TIE2 IN COMPLEX WITH DECIPERA COMPOUND DP1919 -

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Basic information

Entry
Database: PDB / ID: 6mwe
TitleCRYSTAL STRUCTURE OF TIE2 IN COMPLEX WITH DECIPERA COMPOUND DP1919
ComponentsAngiopoietin-1 receptor
KeywordsTRANSFERASE / TIE2 / DP1919 / EMERALDBIO / DECIPHERA
Function / homology
Function and homology information


Tie signaling pathway / regulation of establishment or maintenance of cell polarity / glomerulus vasculature development / regulation of endothelial cell apoptotic process / regulation of vascular permeability / endochondral ossification / heart trabecula formation / definitive hemopoiesis / sprouting angiogenesis / endothelial cell proliferation ...Tie signaling pathway / regulation of establishment or maintenance of cell polarity / glomerulus vasculature development / regulation of endothelial cell apoptotic process / regulation of vascular permeability / endochondral ossification / heart trabecula formation / definitive hemopoiesis / sprouting angiogenesis / endothelial cell proliferation / positive regulation of intracellular signal transduction / positive regulation of Rho protein signal transduction / growth factor binding / positive regulation of Rac protein signal transduction / positive regulation of focal adhesion assembly / microvillus / centriolar satellite / negative regulation of endothelial cell apoptotic process / cell surface receptor protein tyrosine kinase signaling pathway / Tie2 Signaling / response to cAMP / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / negative regulation of angiogenesis / basal plasma membrane / receptor protein-tyrosine kinase / response to peptide hormone / negative regulation of inflammatory response / response to estrogen / positive regulation of angiogenesis / cell-cell junction / cell-cell signaling / heart development / signaling receptor activity / RAF/MAP kinase cascade / basolateral plasma membrane / angiogenesis / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / response to hypoxia / protein kinase activity / positive regulation of protein phosphorylation / membrane raft / apical plasma membrane / focal adhesion / negative regulation of apoptotic process / cell surface / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal / Tie-2 Ig-like domain 1 / Laminin-type EGF domain / Epidermal growth factor-like domain. / EGF-like domain profile. / : / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like domain ...Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal / Tie-2 Ig-like domain 1 / Laminin-type EGF domain / Epidermal growth factor-like domain. / EGF-like domain profile. / : / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like 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. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/Threonine protein kinases, catalytic domain / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-919 / Angiopoietin-1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChun, L. / Abendroth, J. / Edwards, T.E.
CitationJournal: Mol. Cancer Ther. / Year: 2017
Title: The Selective Tie2 Inhibitor Rebastinib Blocks Recruitment and Function of Tie2
Authors: Harney, A.S. / Karagiannis, G.S. / Pignatelli, J. / Smith, B.D. / Kadioglu, E. / Wise, S.C. / Hood, M.M. / Kaufman, M.D. / Leary, C.B. / Lu, W.P. / Al-Ani, G. / Chen, X. / Entenberg, D. / ...Authors: Harney, A.S. / Karagiannis, G.S. / Pignatelli, J. / Smith, B.D. / Kadioglu, E. / Wise, S.C. / Hood, M.M. / Kaufman, M.D. / Leary, C.B. / Lu, W.P. / Al-Ani, G. / Chen, X. / Entenberg, D. / Oktay, M.H. / Wang, Y. / Chun, L. / De Palma, M. / Jones, J.G. / Flynn, D.L. / Condeelis, J.S.
History
DepositionOct 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Angiopoietin-1 receptor
B: Angiopoietin-1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9988
Polymers72,5072
Non-polymers1,4916
Water4,161231
1
A: Angiopoietin-1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9994
Polymers36,2531
Non-polymers7463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Angiopoietin-1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9994
Polymers36,2531
Non-polymers7463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.810, 63.810, 177.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Angiopoietin-1 receptor / Endothelial tyrosine kinase / Tunica interna endothelial cell kinase / Tyrosine kinase with Ig and ...Endothelial tyrosine kinase / Tunica interna endothelial cell kinase / Tyrosine kinase with Ig and EGF homology domains-2 / Tyrosine-protein kinase receptor TEK / Tyrosine-protein kinase receptor TIE-2 / hTIE2 / p140 TEK


Mass: 36253.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEK, TIE2, VMCM, VMCM1 / Plasmid: VCID 2501 / Production host: Trichoptera (caddisflies)
References: UniProt: Q02763, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-919 / 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide / DCC-2036


Mass: 553.587 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H28FN7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: JCSG+ screen e4: 1.26M ammonium sulphate: 200mM lithium sulphate, 100mM Tris pH 8.5: cryo: 25% EG in 3 steps

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.05→45.12 Å / Num. obs: 44133 / % possible obs: 99.5 % / Redundancy: 3.183 % / Biso Wilson estimate: 37.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.061 / Χ2: 0.945 / Net I/σ(I): 18.43
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.308 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.81 / Num. measured obs: 1601 / Num. possible: 521 / Num. unique obs: 484 / CC1/2: 1 / Rrim(I) all: 0.017 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OO8

2oo8


Resolution: 2.05→45.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.501 / SU ML: 0.068 / SU R Cruickshank DPI: 0.0299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.025
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.166 2173 4.9 %RANDOM
Rwork0.148 ---
obs0.149 44082 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.52 Å2 / Biso mean: 36.96 Å2 / Biso min: 16.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å2-0 Å2-0 Å2
2---1.9 Å2-0 Å2
3---3.8 Å2
Refinement stepCycle: final / Resolution: 2.05→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4420 0 102 231 4753
Biso mean--38.29 36.14 -
Num. residues----582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194643
X-RAY DIFFRACTIONr_bond_other_d0.0050.024237
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9536330
X-RAY DIFFRACTIONr_angle_other_deg0.9562.9839655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91923.66194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60515699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5851527
X-RAY DIFFRACTIONr_chiral_restr0.0830.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025309
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021064
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 154 -
Rwork0.178 3081 -
all-3235 -
obs--99.75 %
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)
11.1639-0.34550.50821.1223-0.25681.4846-0.08170.0054-0.00410.02760.1350.01410.0932-0.158-0.05330.0629-0.0725-0.02930.21330.04530.0161-6.31445.24117.417
20.8952-0.2660.46340.8582-0.10442.1141-0.05520.03060.02590.03930.00140.0839-0.1674-0.00460.05380.1771-0.0003-0.02980.0453-0.01030.020514.725.487142.628

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