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(-) Description

Title :  (R)-2-PHENYLPYRROLIDINE SUBSTITUTE IMIDAZOPYRIDAZINES: A NEW CLASS OF POTENT AND SELECTIVE PAN-TRK INHIBITORS
 
Authors :  A. Kreusch, P. Rucker, V. Molteni, J. Loren
Date :  09 Mar 15  (Deposition) - 03 Jun 15  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Trk, Inhibitor, Oncology, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Choi, P. V. Rucker, Z. Wang, Y. Fan, P. Albaugh, G. Chopiuk, F. Gessier, F. Sun, F. Adrian, G. Liu, T. Hood, N. Li, Y. Jia, J. Che, S. Mccormack, A. Li, J. Li, A. Steffy, A. Culazzo, C. Tompkins, V. Phung A. Kreusch, M. Lu, B. Hu, A. Chaudhary, M. Prashad, T. Tuntland, B. Liu, J. Harris, H. M. Seidel, J. Loren, V. Molteni
(R)-2-Phenylpyrrolidine Substituted Imidazopyridazines: A New Class Of Potent And Selective Pan-Trk Inhibitors.
Acs Med. Chem. Lett. V. 6 562 2015
PubMed-ID: 26005534  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00050

(-) 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 Cell Line: SF9
    Expression System Plasmid: PFASTBAC1-HM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    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, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
14EK1Ligand/Ion6-[(2R)-2-(3-FLUOROPHENYL)PYRROLIDIN-1-YL]-3-(PYRIDIN-2-YL)IMIDAZO[1,2-B]PYRIDAZINE
2GOL1Ligand/IonGLYCEROL
3SO45Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:521 , ALA A:542 , PHE A:589 , GLU A:590 , MET A:592 , ARG A:654 , ASN A:655 , CYS A:656 , LEU A:657 , GLY A:667 , ASP A:668 , HOH A:930binding site for residue 4EK A 801
2AC2SOFTWARETHR A:722 , LYS A:725 , ARG A:750 , HOH A:920binding site for residue SO4 A 802
3AC3SOFTWAREARG A:0 , HIS A:503 , HIS A:504 , HOH A:949binding site for residue SO4 A 803
4AC4SOFTWAREARG A:602 , ASP A:607 , TYR A:723 , LYS A:725 , HOH A:973binding site for residue SO4 A 804
5AC5SOFTWAREGLN A:633 , GLY A:661 , LEU A:662binding site for residue SO4 A 805
6AC6SOFTWAREHIS A:571 , SER A:632 , GLN A:633 , HIS A:778 , GLN A:782binding site for residue SO4 A 806
7AC7SOFTWARELYS A:544 , GLU A:560 , ASP A:668 , PHE A:669 , GLY A:670 , MET A:671 , HOH A:929binding site for residue GOL A 807

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1His A:530 -Asn A:531
2Arg A:583 -Pro A:584
3Gly A:613 -Gly A:614

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YNE)

(-) 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:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh.eeeeeeeeee..eeeeeeee.......eeeeeee....hhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee..............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yne A  -4 GSGIRVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPDKMLVAVKALKERQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSTDYYRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLD 793
                                || 506       516       526       538       548|      563       573       583       593       603       613       623       633       643       653       663       678   ||  692       702       712       722       732       742       752       762       772       782       792 
                                0|                             534|        548|                                                                                                                  671|  682|                                                                                                          
                               502                              537         554                                                                                                                   677   687
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4YNE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4YNE)