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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF THE HEPATOCYTE GROWTH FACTOR RECEPTOR C-MET IN COMPLEX WITH ALTIRATINIB ANALOG DP-4157
 
Authors :  B. D. Smith, M. D. Kaufman, C. B. Leary, B. A. Turner, S. A. Wise, Y. M. Ahn, R. J. Booth, T. M. Caldwell, C. L. Ensinger, M. M. Hood, W. -P. Lu, T. W. Pa W. C. Patt, T. J. Rutkoski, T. Samarakoon, H. Telikepalli, L. Vogeti, S K. M. Yates, L. Chun, L. J. Stewart, M. Clare, D. L. Flynn
Date :  27 Aug 15  (Deposition) - 31 Aug 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tyrosine Kinase Domain, Hepatocyte Growth Factor Receptor C-Met, C- Met, Altiratinib Analog, Dp-4157, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. D. Smith, M. D. Kaufman, C. B. Leary, B. A. Turner, S. C. Wise, Y. M. Ahn R. J. Booth, T. M. Caldwell, C. L. Ensinger, M. M. Hood, W. P. Lu, T. W. Patt, W. C. Patt, T. J. Rutkoski, T. Samarakoon, H. Telikepalli, L. Vogeti, S. Vogeti, K. M. Yates, L. Chun, L. J. Stewart, M. Clare, D. L. Flynn
Altiratinib Inhibits Tumor Growth, Invasion, Angiogenesis, And Microenvironment-Mediated Drug Resistance Via Balanced Inhibition Of Met, Tie2, And Vegfr2.
Mol. Cancer Ther. V. 14 2023 2015
PubMed-ID: 26285778  |  Reference-DOI: 10.1158/1535-7163.MCT-14-1105

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR RECEPTOR
    Chains: A, B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: MET
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HGF RECEPTOR,HGF/SF RECEPTOR,PROTO-ONCOGENE C-MET,SCATTER FACTOR RECEPTOR,SF RECEPTOR,TYROSINE-PROTEIN KINASE MET

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
15B42Ligand/IonN-(2,5-DIFLUORO-4-{[2-(1-METHYL-1H-PYRAZOL-4-YL)PYRIDIN-4-YL]OXY}PHENYL)-N'-(4-FLUOROPHENYL)CYCLOPROPANE-1,1-DICARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:1092 , ALA A:1108 , LYS A:1110 , MET A:1131 , VAL A:1139 , LEU A:1140 , LEU A:1157 , PRO A:1158 , TYR A:1159 , MET A:1160 , LYS A:1161 , GLY A:1163 , LEU A:1195 , PHE A:1200 , MET A:1211 , VAL A:1220 , ALA A:1221 , ASP A:1222 , PHE A:1223 , TYR A:1234binding site for residue 5B4 A 1401
2AC2SOFTWAREVAL B:1092 , ALA B:1108 , LYS B:1110 , MET B:1131 , VAL B:1139 , LEU B:1140 , LEU B:1157 , PRO B:1158 , TYR B:1159 , MET B:1160 , LYS B:1161 , GLY B:1163 , LEU B:1195 , PHE B:1200 , MET B:1211 , VAL B:1220 , ALA B:1221 , ASP B:1222 , PHE B:1223 , TYR B:1234binding site for residue 5B4 B 1401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DG5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DG5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DG5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DG5)

(-) Exons   (0, 0)

(no "Exon" information available for 5DG5)

(-) 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:297
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhh..........eee.......eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....ee........ee.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh............hhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dg5 A 1050 TVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG 1346
                                  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       


Chain B from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhh..........eee.......eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....ee........ee.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh............hhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dg5 B 1050 TVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG 1346
                                  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
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 5DG5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DG5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DG5)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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  5dg5
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 Related Entries

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

UniProtKB/Swiss-Prot
        MET_HUMAN | P08581: 1fyr 1r0p 1r1w 1shy 1ssl 1ux3 2cew 2g15 2rfn 2rfs 2uzx 2uzy 2wd1 2wgj 2wkm 3a4p 3bux 3c1x 3ccn 3cd8 3ce3 3cth 3ctj 3dkc 3dkf 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 5eob 5eyc 5eyd 5hlw 5hni 5ho6 5hoa 5hor 5hti 5t3q 5uab 5uad 5uaf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DG5)