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(-) Description

Title :  THE STRUCTURE OF TRKA KINASE BOUND TO THE INHIBITOR 4-NAPHTHALEN-1-YL-1-[(5-PHENYL-1,2,4-OXADIAZOL-3-YL)METHYL]-1H-PYRROLO[3,2-C]PYRIDINE-2-CARBOXYLIC ACID
 
Authors :  H. P. Su
Date :  22 May 14  (Deposition) - 18 Jun 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
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
131X1Ligand/Ion4-(NAPHTHALEN-1-YL)-1-[(5-PHENYL-1,2,4-OXADIAZOL-3-YL)METHYL]-1H-PYRROLO[3,2-C]PYRIDINE-2-CARBOXYLIC ACID
2ACT3Ligand/IonACETATE ION
3CL1Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:524 , ALA A:542 , LYS A:544 , VAL A:573 , PHE A:589 , LEU A:657 , ASP A:668 , PHE A:669 , GLY A:670 , MET A:671binding site for residue 31X A 801
2AC2SOFTWAREPRO A:754 , TYR A:757binding site for residue CL A 802
3AC3SOFTWAREGLY A:625 , ARG A:649 , ARG A:702 , HOH A:903binding site for residue ACT A 803
4AC4SOFTWAREARG A:602 , LYS A:725 , GLN A:726 , TYR A:729binding site for residue ACT A 804
5AC5SOFTWARETRP A:718 , THR A:722 , LYS A:725 , TYR A:729 , PRO A:749 , HOH A:917binding site for residue ACT A 805

(-) SS Bonds  (0, 0)

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

(-) 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 4PMS)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PMS)

(-) 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:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee...eeeeeeee......eeeeeeee...hhhhhhhhhhhhhhh.......eeeee.....eeeeee.....hhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee...hhhhhhhhhhhee...eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pms A 501 CVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLDKMLVAVKALKESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAHHHH 791
                                   510       520       530  ||   543    || 556       566       576       586       596       606       616       626       636       646       656       666       676      |688       698       708       718       728       738       748       758       768       778       788   
                                                          533|        548|                                                                                                                                683|                                                                                                         
                                                           537         552                                                                                                                                 686
   Legend:   → Mismatch (orange background)
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  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 4PMS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 ]  
 

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

(-) Related Entries Specified in the PDB File

4pmm 4pmp 4pmt