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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 :  06 Mar 15  (Deposition) - 03 Jun 15  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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 - NT-3 GROWTH FACTOR RECEPTOR
    Chains: A, B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: [FASTBACT-HM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: NTRK3, TRKC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SEQUENCE REFERS TO NTRK3 ISOFORM B PRECURSOR (NP_002521.2)
    Synonym: GP145-TRKC,TRK-C,NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 3,TRKC TYROSINE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
14EJ2Ligand/Ion4-[6-(BENZYLAMINO)IMIDAZO[1,2-B]PYRIDAZIN-3-YL]BENZONITRILE
2CL1Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
14EJ1Ligand/Ion4-[6-(BENZYLAMINO)IMIDAZO[1,2-B]PYRIDAZIN-3-YL]BENZONITRILE
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
14EJ1Ligand/Ion4-[6-(BENZYLAMINO)IMIDAZO[1,2-B]PYRIDAZIN-3-YL]BENZONITRILE
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:545 , VAL A:552 , ALA A:570 , LYS A:572 , PHE A:617 , GLU A:618 , TYR A:619 , MET A:620 , LEU A:686 , PHE A:698 , GOL A:902binding site for residue 4EJ A 901
2AC2SOFTWARELYS A:572 , GLU A:588 , LEU A:592 , PHE A:617 , GLY A:696 , ASP A:697 , PHE A:698 , 4EJ A:901 , GOL A:903binding site for residue GOL A 902
3AC3SOFTWAREILE A:695 , GLY A:696 , ASP A:697 , GOL A:902binding site for residue GOL A 903
4AC4SOFTWAREARG A:735 , TRP A:754 , TRP A:771 , CYS A:782 , ILE A:783 , ARG A:787 , VAL A:788 , LEU A:789 , TRP A:807 , HOH A:1067binding site for residue GOL A 904
5AC5SOFTWAREARG A:535 , ILE A:538 , LEU A:540 , ARG B:535 , ILE B:538 , LEU B:540binding site for residue CL A 905
6AC6SOFTWAREVAL B:552 , ALA B:570 , LYS B:572 , PHE B:617 , GLU B:618 , TYR B:619 , MET B:620 , GLY B:623 , LEU B:686 , PHE B:698 , MET B:700 , GOL B:902 , HOH B:1048binding site for residue 4EJ B 901
7AC7SOFTWARELYS B:572 , GLY B:696 , ASP B:697 , PHE B:698 , 4EJ B:901 , GOL B:904binding site for residue GOL B 902
8AC8SOFTWAREHIS B:599 , HIS B:658 , GLN B:662 , ASN B:690 , LEU B:691 , LEU B:692binding site for residue GOL B 903
9AC9SOFTWAREILE B:600 , PHE B:675 , ILE B:695 , GLY B:696 , ASP B:697 , GOL B:902 , HOH B:1122binding site for residue GOL B 904

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:611 -Pro A:612
2Thr B:831 -Pro B:832

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YMJ)

(-) Sequences/Alignments

Asymmetric 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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhh.eeeeeeeee...eeeeeeeee.......eeeeeeeee...hhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee......hhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ymj A  -3 GIHVQHIKRRDIVLKRELGEGAFGKVFLAECYNLSPTKDKMLVAVKALKDPTLAARKDFQREAELLTNLQHEHIVKFYGVCGDGDPLIMVFEYMKHGDLNKFLRAHGPGELGLSQMLHIASQIASGMVYLASQHFVHRDLATRNCLVGANLLVKIGDFGDVYsTDYYRHTMLPIRWMPPESIMYRKFTTESDVWSFGVILWEIFTYGKQPWFQLSNTEVIECITQGRVLERPRVCPKEVYDVMLGCWQREPQQRLNIKEIYKILHALGKAT 831
                              ||   536       546       556       566       576       586       596       606       616       626       650       660       670       680       690       703  |    730       740       750       760       770       780       790       800       810       820       830 
                             -1|                                                                                                     634|                                               699|  |  711|                                                                                                      
                             530                                                                                                      649                                                703  |   729                                                                                                      
                                                                                                                                                                                            706-SEP                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eehhh.eeeeeeeee...eeeeeeeee.......eeeeeeeee...hhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.....hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee....hhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ymj B  -3 GIHVQHIKRRDIVLKRELGEGAFGKVFLAECYNLSPTKDKMLVAVKALKDPTLAARKDFQREAELLTNLQHEHIVKFYGVCGDGPLIMVFEYMKHGDLNKFLRAHGPGELGLSQMLHIASQIASGMVYLASQHFVHRDLATRNCLVGANLLVKIGDFGMSRDVYsTDYYRHTMLPIRWMPPESIMYRKFTTESDVWSFGVILWEIFTYGKQPWFQLSNTEVIECITQGRVLERPRVCPKEVYDVMLGCWQREPQQRLNIKEIYKILHALGKATPIY 834
                              ||   536       546       556       566       576       586       596       606   ||  617       627      |651       661       671       681       691       701    |  711|      738       748       758       768       778       788       798       808       818       828      
                             -1|                                                                             610|                   634|                                                      706-SEP1|                                                                                                         
                             530                                                                              612                    649                                                            729
   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 4YMJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (56, 56)

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