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(-) Description

Authors :  J. S. Sack, B. L. Jacobson
Date :  12 Jan 07  (Deposition) - 01 May 07  (Release) - 24 Feb 09  (Revision)
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hormone/Growth Factor, Igf-1R, Kinase Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  U. Velaparthi, M. Wittman, P. Liu, K. Stoffan, K. Zimmermann, X. Sang, J. Carboni, A. Li, R. Attar, M. Gottardis, A. Greer, C. Y. Chang, B. L. Jacobsen, J. S. Sack, Y. Sun, D. R. Langley, B. Balasubramanian, D. Vyas
Discovery And Initial Sar Of 3-(1H-Benzo[D]Imidazol-2-Yl)Pyridin-2(1H)-Ones As Inhibitors Of Insulin-Like Growth Factor 1-Receptor (Igf-1R).
Bioorg. Med. Chem. Lett. V. 17 2317 2007
PubMed-ID: 17317169  |  Reference-DOI: 10.1016/J.BMCL.2007.01.102
(for further references see the PDB file header)

(-) Compounds

    EC Number2.7.1.112
    Expression System Taxid10469
    Expression System Vector TypeBACULOVIRUS
    FragmentKINASE DOMAIN, RESIDUES 982-1286
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCD221 ANTIGEN, IGF1R

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
1AC1SOFTWAREHOH A:112 , LEU A:975 , ALA A:1001 , MET A:1049 , GLU A:1050 , LEU A:1051 , MET A:1052 , THR A:1053 , GLY A:1055 , MET A:1112 , THR A:1127BINDING SITE FOR RESIDUE BMI A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OJ9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
1Gln A:1043 -Pro A:1044

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076249R1256SIGF1R_HUMANDisease (IGF1RES)  ---AR1226S

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.IGF1R_HUMAN1005-1033  1A:975-1003
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.IGF1R_HUMAN1131-1143  1A:1101-1113
3RECEPTOR_TYR_KIN_IIPS00239 Receptor tyrosine kinase class II signature.IGF1R_HUMAN1159-1167  1A:1129-1137

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:295
 aligned with IGF1R_HUMAN | P08069 from UniProtKB/Swiss-Prot  Length:1367

    Alignment length:303
                                   993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283   
               SCOP domains d2oj9a_ A: Insulin-like growth factor 1 receptor                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2oj9A01 A:954-1048 Phosphorylase Kinase; domain 1                                              2oj9A02 A:1049-1249         Transferase(Phosphotransferase) domain 1                                                                                                                                     ------- CATH domains
               Pfam domains ---------------Pkinase_Tyr-2oj9A01 A:969-1236                                                                                                                                                                                                                                              -------------------- Pfam domains
         Sec.struct. author ...........hhh.eeeeeeeee....eeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh....--------..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.........hhhhheee...eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------ SAPs(SNPs)
                    PROSITE ---------------------PROTEIN_KINASE_ATP           -------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------RECEPTOR_----------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1----------------------------------------------------------------------------Exon 1.17  PDB: A:1033-1067          Exon 1.18  PDB: A:1076-1123 UniProt: 1100-1153        ------------------------------------------Exon 1.20  PDB: A:1166-1211 UniProt: 1196-1241--------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.16  PDB: A:956-1032 UniProt: 986-1062                                 ------------------------------------------------------------------------------------------Exon 1.19  PDB: A:1123-1166                 --------------------------------------------Exon 1.21b  PDB: A:1211-1256 [INCOMPLETE]      Transcript 1 (2)
                                   963       973       983       993      1003      1013      1023      1033      1043      1053      1063   |     -  |   1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253   
                                                                                                                                          1067     1076                                                                                                                                                                                    

   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  (2, 2)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
Clan: PKinase (934)

(-) Gene Ontology  (41, 41)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IGF1R_HUMAN | P08069)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0043559    insulin binding    Interacting selectively and non-covalently with insulin, a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0005158    insulin receptor binding    Interacting selectively and non-covalently with the insulin receptor.
    GO:0043560    insulin receptor substrate binding    Interacting selectively and non-covalently with any of the insulin receptor substrate (IRS) proteins, adaptor proteins that bind to the transphosphorylated insulin and insulin-like growth factor receptors, are themselves phosphorylated and in turn recruit SH2 domain-containing signaling molecules to form a productive signaling complex.
    GO:0031994    insulin-like growth factor I binding    Interacting selectively and non-covalently with insulin-like growth factor I.
    GO:0005520    insulin-like growth factor binding    Interacting selectively and non-covalently with an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it.
    GO:0005010    insulin-like growth factor-activated receptor activity    Combining with insulin-like growth factor and transmitting the signal across the plasma membrane 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:0043548    phosphatidylinositol 3-kinase binding    Interacting selectively and non-covalently with a phosphatidylinositol 3-kinase, any enzyme that catalyzes the addition of a phosphate group to an inositol lipid at the 3' position of the inositol ring.
    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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0051389    inactivation of MAPKK activity    Any process that terminates the activity of the active enzyme MAP kinase kinase (MAPKK).
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0048009    insulin-like growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin-like growth factor receptor binding to one of its physiological ligands.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    GO:0014065    phosphatidylinositol 3-kinase signaling    A series of reactions within the signal-receiving cell, mediated by the intracellular phosphatidylinositol 3-kinase (PI3K). Many cell surface receptor linked signaling pathways signal through PI3K to regulate numerous cellular functions.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    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:0045740    positive regulation of DNA replication    Any process that activates or increases the frequency, rate or extent of DNA replication.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    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:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0046328    regulation of JNK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    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:0035867    alphav-beta3 integrin-IGF-1-IGF1R complex    A protein complex that consists of an alphav-beta3 integrin complex bound to insulin-like growth factor-1 (IGF-1) and type I insulin-like growth factor receptor (IGF1R). IGF1R is a heterotetramer that consists of two alpha-subunits and two beta-subunits.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma 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.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.


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 Related Entries

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

        IGF1R_HUMAN | P080691igr 1jqh 1k3a 1m7n 1p4o 2zm3 3d94 3f5p 3i81 3lvp 3lw0 3nw5 3nw6 3nw7 3o23 3qqu 4d2r 4xss 5fxq 5fxr 5fxs 5hzn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OJ9)