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(-) Description

Title :  THE STRUCTURE OF TRKA KINASE BOUND TO THE INHIBITOR 1-CYCLOPROPYL-1-[3-(1,3-THIAZOL-2-YL)BENZYL]-3-[4-(TRIFLUOROMETHOXY)PHENYL]UREA
 
Authors :  H. P. Su
Date :  22 May 14  (Deposition) - 18 Jun 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Stachel, J. M. Sanders, D. A. Henze, M. T. Rudd, H. P. Su, Y. Li, K. K. Nanda, M. S. Egbertson, P. J. Manley, K. L. Jones, E. J. Brnardic, A. Green, J. A. Grobler, B. Hanney, M. Leitl, M. T. Lai, V. Munshi, D. Murphy, K. Rickert, D. Riley, A. Krasowska-Zoladek, C. Daley, P. Zuck, S. A. Kane, M. T. Bilodeau
Maximizing Diversity From A Kinase Screen: Identification O Novel And Selective Pan-Trk Inhibitors For Chronic Pain.
J. Med. Chem. V. 57 5800 2014
PubMed-ID: 24914455  |  Reference-DOI: 10.1021/JM5006429

(-) 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: KINASE DOMAIN (UNP RESIDUES 501-787)
    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  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
131W1Ligand/Ion1-CYCLOPROPYL-1-[3-(1,3-THIAZOL-2-YL)BENZYL]-3-[4-(TRIFLUOROMETHOXY)PHENYL]UREA
2ACT3Ligand/IonACETATE ION
3CL1Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:542 , LEU A:564 , LEU A:567 , VAL A:573 , PHE A:589 , GLU A:590 , TYR A:591 , MET A:592 , LEU A:657 , ILE A:666 , GLY A:667 , ASP A:668binding site for residue 31W A 801
2AC2SOFTWAREALA A:758 , ARG A:761 , HOH A:929binding site for residue CL A 802
3AC3SOFTWAREGLY A:625 , ARG A:649 , ARG A:702 , HOH A:904 , HOH A:937binding site for residue ACT A 803
4AC4SOFTWAREARG A:602 , LYS A:725 , GLN A:726 , TYR A:729 , HOH A:1035binding site for residue ACT A 804
5AC5SOFTWARETRP A:718 , LYS A:725 , TYR A:729 , HOH A:1010 , HOH A:1069binding site for residue ACT A 805

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PMP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:583 -Pro A:584
2Val A:683 -Gly A:684

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PMP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PMP)

(-) Exons   (0, 0)

(no "Exon" information available for 4PMP)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eeeeeeeee...eeeeeeee......eeeeeee..hhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee........hhhhhee...eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pmp A 501 CVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLKMLVAVKALKSARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRIYSTDYYRVGTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAHHHH 791
                                   510       520       530  ||   544  ||   558       568       578       588       598       608       618       628       638       648       658       668    || 679    || 691       701       711       721       731       741       751       761       771       781       791
                                                          533|      547|                                                                                                                      673|      684|                                                                                                        
                                                           538       552                                                                                                                       675       687
   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  (0, 0)

(no "SCOP Domain" information available for 4PMP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PMP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PMP)

(-) Gene Ontology  (88, 88)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:583 - Pro A:584   [ RasMol ]  
    Val A:683 - Gly A:684   [ RasMol ]  
 

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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 4pms 4pmt 4yne 4yps 5h3q 5jfs 5jfv 5jfw 5jfx 5kmi 5kmj 5kmk 5kml 5kmm 5kmn 5kmo

(-) Related Entries Specified in the PDB File

4pmm 4pms 4pmt