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(-) Description

Title :  STRUCTURE OF MET RECEPTOR TYROSINE KINASE IN COMPLEX WITH INHIBITOR SGX-523
 
Authors :  J. Hendle
Date :  24 Jun 08  (Deposition) - 07 Jul 09  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Drug Discovery, C-Met Kinase, Fragment Based, Membrane, Receptor, Transmembrane, Oncoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. G. Buchanan, J. Hendle, P. S. Lee, C. R. Smith, P. Y. Bounaud, K. A. Jessen, C. M. Tang, N. H. Huser, J. D. Felce, K. J. Froning, M. C. Peterman, B. E. Aubol, S. F. Gessert, J. M. Sauder, K. D. Schwinn, M. Russell, I. A. Rooney, J. Adams, B. C. Leon, T. H. Do, J. M. Blaney, P. A. Sprengeler, D. A. Thompson, L. Smyth, L. A. Pelletier, S. Atwell, K. Holme, S. R. Wasserman, S. Emtage, S. K. Burley, S. H. Reich
Sgx523 Is An Exquisitely Selective, Atp-Competitive Inhibitor Of The Met Receptor Tyrosine Kinase With Antitumo Activity In Vivo.
Mol. Cancer Ther. V. 8 3181 2009
PubMed-ID: 19934279  |  Reference-DOI: 10.1158/1535-7163.MCT-09-0477

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneMET, HCG_38705, TCAG7.66
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHGF RECEPTOR, HGF/SF RECEPTOR, PROTO-ONCOGENE C-MET, SCATTER FACTOR RECEPTOR, SF RECEPTOR, TYROSINE-PROTEIN KINASE MET

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SX81Ligand/Ion6-{[6-(1-METHYL-1H-PYRAZOL-4-YL)[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-3-YL]SULFANYL}QUINOLINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:1179 , GLY A:1346 , GLU A:1347 , HIS A:1348BINDING SITE FOR RESIDUE CL A 2
2AC2SOFTWAREILE A:1084 , ALA A:1108 , PRO A:1158 , TYR A:1159 , MET A:1160 , ASP A:1164 , ARG A:1208 , MET A:1211 , ALA A:1221 , ASP A:1222 , ALA A:1226 , TYR A:1230BINDING SITE FOR RESIDUE SX8 A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DKF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DKF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (19, 19)

Asymmetric/Biological Unit (19, 19)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_032485V1092IMET_HUMANDisease (RCCP)786202724AV1092I
02UniProtVAR_032486H1094LMET_HUMANDisease (RCCP)  ---AH1094L
03UniProtVAR_032487H1094RMET_HUMANDisease (RCCP)121913243AH1094R
04UniProtVAR_032488H1094YMET_HUMANDisease (RCCP)121913244AH1094Y
05UniProtVAR_032489H1106DMET_HUMANDisease (RCCP)  ---AH1106D
06UniProtVAR_006286M1131TMET_HUMANDisease (RCCP)121913668AM1131T
07UniProtVAR_032490T1173IMET_HUMANDisease (HCC)121913675AT1173I
08UniProtVAR_006287V1188LMET_HUMANDisease (RCCP)121913669AV1188L
09UniProtVAR_006288L1195VMET_HUMANDisease (RCCP)121913673AL1195V
10UniProtVAR_006289V1220IMET_HUMANDisease (RCCP)121913670AV1220I
11UniProtVAR_006291D1228HMET_HUMANDisease (RCCP)  ---AD1228H
12UniProtVAR_006290D1228NMET_HUMANDisease (RCCP)121913671AD1228N
13UniProtVAR_006292Y1230CMET_HUMANDisease (RCCP)121913246AY1230C
14UniProtVAR_032491Y1230DMET_HUMANDisease (RCCP)  ---AY1230D
15UniProtVAR_006293Y1230HMET_HUMANDisease (RCCP)121913247AY1230H
16UniProtVAR_032492K1244RMET_HUMANDisease (HCC)121913677AK1244R
17UniProtVAR_032493M1250IMET_HUMANDisease (HCC)121913676AM1250I
18UniProtVAR_006294M1250TMET_HUMANDisease (RCCP)121913245AM1250T
19UniProtVAR_064857V1294IMET_HUMANUnclassified  ---AV1294I

  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.MET_HUMAN1084-1110  1A:1084-1110
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.MET_HUMAN1200-1212  1A:1200-1212

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003977521cENSE00001865305chr7:116312446-116312631186MET_HUMAN-00--
1.3cENST000003977523cENSE00001238915chr7:116339125-1163403381214MET_HUMAN1-4004000--
1.6ENST000003977526ENSE00000717722chr7:116371722-116371913192MET_HUMAN401-464640--
1.7ENST000003977527ENSE00000717724chr7:116380004-116380138135MET_HUMAN465-509450--
1.8ENST000003977528ENSE00000717726chr7:116380906-116381079174MET_HUMAN510-567580--
1.9bENST000003977529bENSE00000717728chr7:116395409-116395569161MET_HUMAN568-621540--
1.10ENST0000039775210ENSE00000717730chr7:116397491-116397593103MET_HUMAN621-655350--
1.11bENST0000039775211bENSE00000717732chr7:116397692-116397828137MET_HUMAN656-701460--
1.12aENST0000039775212aENSE00000717735chr7:116398513-116398674162MET_HUMAN701-755550--
1.13bENST0000039775213bENSE00001530016chr7:116399445-116399544100MET_HUMAN755-788340--
1.14ENST0000039775214ENSE00000717791chr7:116403104-116403322219MET_HUMAN789-861730--
1.15aENST0000039775215aENSE00000717803chr7:116409699-116409845147MET_HUMAN862-910490--
1.16ENST0000039775216ENSE00000717811chr7:116411552-116411708157MET_HUMAN911-963530--
1.17ENST0000039775217ENSE00000717833chr7:116411903-116412043141MET_HUMAN963-1010480--
1.18bENST0000039775218bENSE00000717861chr7:116414935-116415165231MET_HUMAN1010-1087781A:1050-108738
1.19ENST0000039775219ENSE00000717879chr7:116417443-11641752381MET_HUMAN1087-1114281A:1087-1114 (gaps)28
1.20ENST0000039775220ENSE00000717895chr7:116418830-116419011182MET_HUMAN1114-1174611A:1114-117461
1.21ENST0000039775221ENSE00000717902chr7:116422042-116422151110MET_HUMAN1175-1211371A:1175-121137
1.22ENST0000039775222ENSE00000717928chr7:116423358-116423523166MET_HUMAN1211-1266561A:1211-1266 (gaps)56
1.23ENST0000039775223ENSE00000717937chr7:116435709-116435845137MET_HUMAN1267-1312461A:1267-131246
1.24bENST0000039775224bENSE00000881894chr7:116435941-1164384402500MET_HUMAN1312-1390791A:1312-136150

(-) 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:294
 aligned with MET_HUMAN | P08581 from UniProtKB/Swiss-Prot  Length:1390

    Alignment length:312
                                  1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359  
           MET_HUMAN   1050 TVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHVNATYVNVKC 1361
               SCOP domains d3dkfa_ A: Hepatocyte growth factor receptor, c-     MET                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -----------3dkfA01 A:1061-1159 Phosphorylase Kin     ase; domain 1                                            3dkfA02 A:1160-1361 Transferase(Phosphotransferase) domain 1                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh......eeeeeeeeeee..eeeeeeee-----..eeeeeeee....hhhhhhhhhhhhhhhhh..........eeeee...eeeeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..hhhhh...-------------..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.................. Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------I-L-----------D------------------------T-----------------------------------------I--------------L------V------------------------I-------H-C-------------R-----I-------------------------------------------I------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------R-------------------------------------------------------------------------------------------------------------------------------------N-D-------------------T--------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------Y---------------------------------------------------------------------------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ----------------------------------PROTEIN_KINASE_ATP         -----------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18b  PDB: A:1050-1087          --------------------------Exon 1.20  PDB: A:1114-1174 UniProt: 1114-1174               Exon 1.21  PDB: A:1175-1211          -------------------------------------------------------Exon 1.23  PDB: A:1267-1312 UniProt: 1267-1312------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.19 UniProt: 1087-1114------------------------------------------------------------------------------------------------Exon 1.22  PDB: A:1211-1266 (gaps) UniProt: 1211-1266   ---------------------------------------------Exon 1.24b  PDB: A:1312-1361 UniProt: 1312-1390    Transcript 1 (2)
                3dkf A 1050 TVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTL-----KKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKFLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMY-------------KLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHVNATYVNVKE 1361
                                  1059      1069      1079      1089       | -   |  1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229|        -    | 1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359  
                                                                        1097  1103                                                                                                                           1230          1244                                                                                                                     

   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  (0, 0)

(no "Pfam Domain" information available for 3DKF)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MET_HUMAN | P08581)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005008    hepatocyte growth factor-activated receptor activity    Combining with hepatocyte 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: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:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    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:0048754    branching morphogenesis of an epithelial tube    The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0001886    endothelial cell morphogenesis    The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell.
    GO:0048012    hepatocyte growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of the hepatocyte growth factor receptor binding to one of its physiological ligands.
    GO:0010507    negative regulation of autophagy    Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:1901299    negative regulation of hydrogen peroxide-mediated programmed cell death    Any process that stops, prevents or reduces the frequency, rate or extent of hydrogen peroxide-mediated programmed cell death.
    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:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:2001028    positive regulation of endothelial cell chemotaxis    Any process that activates or increases the frequency, rate or extent of endothelial cell chemotaxis.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0071526    semaphorin-plexin signaling pathway    A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
    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:0009925    basal plasma membrane    The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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
        MET_HUMAN | P085811fyr 1r0p 1r1w 1shy 1ssl 1ux3 2cew 2g15 2rfn 2rfs 2uzx 2uzy 2wd1 2wgj 2wkm 3a4p 3bux 3c1x 3ccn 3cd8 3ce3 3cth 3ctj 3dkc 3dkg 3efj 3efk 3f66 3f82 3i5n 3l8v 3lq8 3q6u 3q6w 3qti 3r7o 3rhk 3u6h 3u6i 3vw8 3zbx 3zc5 3zcl 3zxz 3zze 4aoi 4ap7 4deg 4deh 4dei 4eev 4gg5 4gg7 4iwd 4k3j 4knb 4mxc 4o3t 4o3u 4r1v 4r1y 4xmo 4xyf 5dg5 5eob 5eyc 5eyd 5hlw 5hni 5ho6 5hoa 5hor 5hti 5t3q 5uab 5uad 5uaf

(-) Related Entries Specified in the PDB File

3dkc STRUCTURE OF MET RECEPTOR TYROSINE KINASE IN COMPLEX WITH ATP
3dkg STRUCTURE OF MUTANT(Y1248L) MET RECEPTOR TYROSINE KINASE IN COMPLEX WITH INHIBITOR SGX-523