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- PDB-8bm8: Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase wi... -

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Basic information

Entry
Database: PDB / ID: 8bm8
TitleCrystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 11
ComponentsEphrin type-A receptor 2
KeywordsTRANSFERASE / Inhibitor / Complex / Protein Tyrosine Kinase
Function / homology
Function and homology information


notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / leading edge membrane ...notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / leading edge membrane / negative regulation of chemokine production / ephrin receptor activity / activation of GTPase activity / post-anal tail morphogenesis / response to growth factor / positive regulation of bicellular tight junction assembly / bone remodeling / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / negative regulation of cell adhesion mediated by integrin / EPH-Ephrin signaling / central nervous system neuron differentiation / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / neural tube development / mammary gland epithelial cell proliferation / tight junction / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / vasculogenesis / regulation of ERK1 and ERK2 cascade / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / osteoclast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / molecular function activator activity / negative regulation of angiogenesis / protein localization to plasma membrane / cell chemotaxis / skeletal system development / positive regulation of protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / intrinsic apoptotic signaling pathway in response to DNA damage / ruffle membrane / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / cell adhesion / signaling receptor complex / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 2, ligand binding domain / Ephrin cysteine rich domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. ...Ephrin type-A receptor 2, ligand binding domain / Ephrin cysteine rich domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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
Similarity search - Domain/homology
: / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLinhard, V. / Witt, K. / Gande, S. / Wollenhaupt, J. / Lennartz, F. / Weiss, M.S. / Schwalbe, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Chemistry / Year: 2023
Title: Optimization of the Lead Compound NVP-BHG712 as a Colorectal Cancer Inhibitor.
Authors: Troster, A. / DiPrima, M. / Jores, N. / Kudlinzki, D. / Sreeramulu, S. / Gande, S.L. / Linhard, V. / Ludig, D. / Schug, A. / Saxena, K. / Reinecke, M. / Heinzlmeir, S. / Leisegang, M.S. / ...Authors: Troster, A. / DiPrima, M. / Jores, N. / Kudlinzki, D. / Sreeramulu, S. / Gande, S.L. / Linhard, V. / Ludig, D. / Schug, A. / Saxena, K. / Reinecke, M. / Heinzlmeir, S. / Leisegang, M.S. / Wollenhaupt, J. / Lennartz, F. / Weiss, M.S. / Kuster, B. / Tosato, G. / Schwalbe, H.
History
DepositionNov 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 4, 2026Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9232
Polymers34,4631
Non-polymers4601
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.540, 106.430, 40.250
Angle α, β, γ (deg.)90.000, 108.440, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 34462.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Chemical ChemComp-QT1 / ~{N}-(3-cyanophenyl)-4-methyl-3-[(1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]benzamide


Mass: 460.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H20N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.92 Å3/Da / Density % sol: 35.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 37,5 % MPD_PEG1000_PEG3350, 100 mM Morpheus Amino Acids Mix, 100 mM Bis-Tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.68→38.18 Å / Num. obs: 28709 / % possible obs: 96.5 % / Redundancy: 3.32 % / Biso Wilson estimate: 18.69 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.141 / Net I/σ(I): 7.75
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 3.17 % / Num. unique obs: 4461 / CC1/2: 0.414 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6q7d

6q7d


Resolution: 1.68→38.18 Å / SU ML: 0.2629 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.5677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 1434 5 %
Rwork0.1897 27262 -
obs0.1915 28696 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.45 Å2
Refinement stepCycle: LAST / Resolution: 1.68→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 35 102 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652427
X-RAY DIFFRACTIONf_angle_d0.98883298
X-RAY DIFFRACTIONf_chiral_restr0.0534342
X-RAY DIFFRACTIONf_plane_restr0.0126507
X-RAY DIFFRACTIONf_dihedral_angle_d7.3227400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.740.40741360.35392590X-RAY DIFFRACTION91.17
1.74-1.810.33471420.29322713X-RAY DIFFRACTION96.29
1.81-1.890.26941420.2442691X-RAY DIFFRACTION96.92
1.89-1.990.26611450.22892743X-RAY DIFFRACTION97.27
1.99-2.110.24221440.20482753X-RAY DIFFRACTION97.51
2.11-2.280.24071450.19162749X-RAY DIFFRACTION97.74
2.28-2.510.241450.18342742X-RAY DIFFRACTION97.07
2.51-2.870.23071450.17392768X-RAY DIFFRACTION98.21
2.87-3.610.21151460.16662773X-RAY DIFFRACTION97.69
3.61-38.180.16521440.15762740X-RAY DIFFRACTION96.29
Refinement TLS params.Method: refined / Origin x: -81.5072974037 Å / Origin y: -8.09266123959 Å / Origin z: 90.1443138113 Å
111213212223313233
T0.104897645156 Å20.00961510640978 Å2-0.0056468846656 Å2-0.229881248761 Å20.00258954385449 Å2--0.122799541897 Å2
L0.475543450932 °20.245542237659 °20.0121755134456 °2-1.18715746591 °2-0.0817642160776 °2--0.33631906278 °2
S-0.0131125748523 Å °-0.0226129815314 Å °-0.0489833169387 Å °-0.0182167376159 Å °0.0247985017478 Å °-0.0528882142982 Å °0.0337412718662 Å °0.0324040774483 Å °-0.0196650922217 Å °
Refinement TLS groupSelection details: (chain A and resid 605:895)

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