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(-) Description

Title :  TRKA JM-KINASE WITH 1-(9{H}-FLUOREN-9-YL)-3-(2-METHYL-4-PHENYL-PYRIMIDIN-5-YL)UREA
 
Authors :  H. P. Su
Date :  27 Jun 16  (Deposition) - 28 Dec 16  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Juxtamembrane, Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. Su, K. Rickert, C. Burlein, K. Narayan, M. Bukhtiyarova, D. M. Hurzy, C. A. Stump, X. Zhang, J. Reid, A. Krasowska-Zoladek, S. Tummala, J. M. Shipman, M. Kornienko, P. A. Lemaire, D. Krosky, A. Heller, A. Achab, C. Chamberlin, P. Saradjian, B. Sauvagnat, X. Yang, M. R. Ziebell, E. Nickbarg, J. M. Sanders, M. T. Bilodeau, S. S. Carroll, K. J. Lumb, S. M. Soisson, D. A. Henze, A. J. Cooke
Structural Characterization Of Nonactive Site, Trka-Selective Kinase Inhibitors.
Proc. Natl. Acad. Sci. V. 114 E297 2017 U. S. A.
PubMed-ID: 28039433  |  Reference-DOI: 10.1073/PNAS.1611577114

(-) Compounds

Molecule 1 - HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: CATALYTIC DOMAIN WITH JUXTAMEMBRANE REGION, UNP RESIDUES 376-698
    Gene: NTRK1, MTC, TRK, TRKA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 1,TRK1- TRANSFORMING TYROSINE KINASE PROTEIN,TROPOMYOSIN-RELATED KINASE A, TYROSINE KINASE RECEPTOR,TYROSINE KINASE RECEPTOR A,TRK-A,GP140TRK, P140-TRKA

 Structural Features

(-) Chains, Units

  1
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
16UE1Ligand/Ion1-(9~{H}-FLUOREN-9-YL)-3-(2-METHYL-4-PHENYL-PYRIMIDIN-5-YL)UREA

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:488 , HIS A:489 , ILE A:490 , PHE A:521 , LYS A:544 , GLU A:560 , LEU A:564 , LEU A:567 , HIS A:648 , ASP A:668 , GLY A:670binding site for residue 6UE A 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:583 -Pro A:584

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KMI)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.......hhh.eeeeeeeeee..eeeeeeeee.......eeeeeeeee..hhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee....hhhhhhhhhheee...eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kmi A 486 LQGHIIENPQCVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG 796
                                   495|      510       520       530       540      |553       563       573       583       593       603      |616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796
                                   495|                                           547|                                                        610|                                                                                                                                                                                      
                                    501                                            551                                                         614
   Legend:   → Mismatch (orange background)
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  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 5KMI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (88, 88)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NTRK1_HUMAN | P04629: 1he7 1shc 1wwa 1www 2ifg 2n90 4aoj 4crp 4f0i 4gt5 4pmm 4pmp 4pms 4pmt 4yne 4yps 5h3q 5jfs 5jfv 5jfw 5jfx 5kmj 5kmk 5kml 5kmm 5kmn 5kmo

(-) Related Entries Specified in the PDB File

5kmj 5kmk 5kml 5kmm 5kmn 5kmo