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(-) Description

Title :  EPHB4 KINASE DOMAIN INHIBITOR COMPLEX
 
Authors :  J. Read, C. A. Brassington, I. Green, E. J. Mccall, A. L. Valentine, D. B
Date :  17 Mar 10  (Deposition) - 29 Sep 10  (Release) - 20 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Atp-Binding, Glycoprotein, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Bardelle, B. Barlaam, N. Brooks, T. Coleman, D. Cross, R. Ducray, I. Green, C. L. Brempt, A. Olivier, J. Read
Inhibitors Of The Tyrosine Kinase Ephb4. Part 3: Identification Of Non-Benzodioxole-Based Kinase Inhibitors.
Bioorg. Med. Chem. Lett. V. 20 6242 2010
PubMed-ID: 20850301  |  Reference-DOI: 10.1016/J.BMCL.2010.08.100

(-) Compounds

Molecule 1 - EPHRIN TYPE-B RECEPTOR 4
    ChainsA
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF21
    Expression System PlasmidPFASTBAC
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentKINASE DOMAIN, RESIDUES 598-899
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEPHB4 RECEPTOR TYROSINE KINASE, TYROSINE-PROTEIN KINASE RECEPTOR HTK, TYROSINE-PROTEIN KINASE TYRO11

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2X9F1Ligand/IonN^4^-1H-INDAZOL-4-YL-N^2^-[3-(METHYLSULFONYL)PHENYL]PYRIMIDINE-2,4-DIAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:621 , GLY A:622 , VAL A:629 , ALA A:645 , LYS A:647 , GLU A:664 , THR A:693 , GLU A:694 , PHE A:695 , MET A:696 , GLU A:697 , GLY A:699 , LEU A:747 , SER A:757 , ASP A:758 , HOH A:2023 , HOH A:2242 , HOH A:2243BINDING SITE FOR RESIDUE X9F A1889
2AC2SOFTWAREASP A:740 , ASP A:758 , MG A:1891 , HOH A:2029 , HOH A:2030 , HOH A:2032 , HOH A:2127BINDING SITE FOR RESIDUE MG A1890
3AC3SOFTWAREASP A:740 , ASP A:758 , MG A:1890 , HOH A:2109 , HOH A:2126 , HOH A:2127BINDING SITE FOR RESIDUE MG A1891

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X9F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:687 -Pro A:688

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042186R678HEPHB4_HUMANPolymorphism55692440AR678H
2UniProtVAR_078063R739QEPHB4_HUMANDisease (HFASD)  ---AR739Q
3UniProtVAR_078064I782SEPHB4_HUMANDisease (HFASD)  ---AI782S
4UniProtVAR_042187A882TEPHB4_HUMANPolymorphism34918225AA882T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.EPHB4_HUMAN621-647  1A:621-647
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.EPHB4_HUMAN736-748  1A:736-748

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003581731bENSE00001868923chr7:100425121-100424601521EPHB4_HUMAN1-18180--
1.2bENST000003581732bENSE00000825052chr7:100421895-10042182571EPHB4_HUMAN18-41240--
1.3ENST000003581733ENSE00000825051chr7:100421553-100421266288EPHB4_HUMAN42-137960--
1.4ENST000003581734ENSE00000825050chr7:100420289-100419893397EPHB4_HUMAN138-2701330--
1.5bENST000003581735bENSE00000825049chr7:100417918-100417763156EPHB4_HUMAN270-322530--
1.6ENST000003581736ENSE00000825048chr7:100417511-100417179333EPHB4_HUMAN322-4331120--
1.7bENST000003581737bENSE00000710240chr7:100416266-100416142125EPHB4_HUMAN433-474420--
1.8cENST000003581738cENSE00001706820chr7:100414979-100414814166EPHB4_HUMAN475-530560--
1.9cENST000003581739cENSE00001665919chr7:100411643-100411541103EPHB4_HUMAN530-564350--
1.10ENST0000035817310ENSE00001787983chr7:100411338-10041127465EPHB4_HUMAN564-586230--
1.11bENST0000035817311bENSE00001754468chr7:100410830-100410717114EPHB4_HUMAN586-624391A:608-62417
1.12ENST0000035817312ENSE00001631272chr7:100410616-100410369248EPHB4_HUMAN624-706831A:624-706 (gaps)83
1.13aENST0000035817313aENSE00001753966chr7:100405202-100404987216EPHB4_HUMAN707-778721A:707-76559
1.14aENST0000035817314aENSE00001623534chr7:100404191-100404042150EPHB4_HUMAN779-828501A:779-82850
1.15ENST0000035817315ENSE00001783205chr7:100403316-100403123194EPHB4_HUMAN829-893651A:829-88860
1.16ENST0000035817316ENSE00001649970chr7:100402943-100402788156EPHB4_HUMAN893-945530--
1.17bENST0000035817317bENSE00001639386chr7:100401212-1004001871026EPHB4_HUMAN945-987430--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:265
 aligned with EPHB4_HUMAN | P54760 from UniProtKB/Swiss-Prot  Length:987

    Alignment length:281
                                   617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887 
          EPHB4_HUMAN   608 KEIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLKGGYTERQRREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFGLSRFLEENSSDPTYTSSLGGKIPIRWTAPEAIAFRKFTSASDAWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQVVSALDKMIRNPASLKIVA 888
               SCOP domains d2x9fa_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------Pkinase_Tyr-2x9fA01 A:615-874                                                                                                                                                                                                                                       -------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeeee....eeeeeee.......eeeeeeee---.hhhhhhhhhhhhhhhh.........eeeee.....eeeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.........-------------....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------H------------------------------------------------------------Q------------------------------------------S---------------------------------------------------------------------------------------------------T------ SAPs(SNPs)
                    PROSITE -------------PROTEIN_KINASE_ATP         ----------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11b       ----------------------------------------------------------------------------------Exon 1.13a  PDB: A:707-765 UniProt: 707-778 [INCOMPLETE]                Exon 1.14a  PDB: A:779-828 UniProt: 779-828       Exon 1.15  PDB: A:829-888 UniProt: 829-893 [INCOMPLETE]      Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.12  PDB: A:624-706 (gaps) UniProt: 624-706                                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2x9f A 608 KEIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTL---YTERQRREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFGLSRFL-------------GGKIPIRWTAPEAIAFRKFTSASDAWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQVVSALDKMIRNPASLKIVA 888
                                   617       627       637       647 |   | 657       667       677       687       697       707       717       727       737       747       757       | -         - |     787       797       807       817       827       837       847       857       867       877       887 
                                                                   649 653                                                                                                             765           779                                                                                                             

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X9F)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EPHB4_HUMAN | P54760)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005003    ephrin receptor activity    Combining with an ephrin to initiate a change in cell activity.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0002042    cell migration involved in sprouting angiogenesis    The orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels involved in sprouting angiogenesis.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EPHB4_HUMAN | P547602bba 2e7h 2hle 2qkq 2vwu 2vwv 2vww 2vwx 2vwy 2vwz 2vx0 2vx1 2xvd 2yn8 3zew 4aw5 4bb4

(-) Related Entries Specified in the PDB File

2bba CRYSTAL STRUCTURE AND THERMODYNAMIC CHARACTERIZATION OF THEEPHB4 RECEPTOR IN COMPLEX WITH AN EPHRIN-B2 ANTAGONISTPEPTIDE REVEALS THE DETERMINANTS FOR RECEPTOR SPECIFICITY
2vwu EPHB4 KINASE DOMAIN INHIBITOR COMPLEX
2vwv EPHB4 KINASE DOMAIN INHIBITOR COMPLEX
2vww EPHB4 KINASE DOMAIN INHIBITOR COMPLEX
2vwx EPHB4 KINASE DOMAIN INHIBITOR COMPLEX
2vwy EPHB4 KINASE DOMAIN INHIBITOR COMPLEX
2vwz EPHB4 KINASE DOMAIN INHIBITOR COMPLEX
2vx0 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX
2vx1 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX