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(-) Description

Title :  FRAGMENT-BASED DISCOVERY OF POTENT AND SELECTIVE DDR1/2 INHIBITORS
 
Authors :  C. Murray, V. Berdini, I. Buck, M. Carr, A. Cleasby, J. Coyle, J. Curry, J K. Hearn, A. Iqbal, L. Lee, V. Martins, P. Mortenson, J. Munck, L. Page, S. Roomans, T. Kirsten, G. Saxty
Date :  05 Jun 15  (Deposition) - 12 Aug 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  A
Keywords :  Ddr1, Fragments, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. W. Murray, V. Berdini, I. M. Buck, M. E. Carr, A. Cleasby, J. E. Coyle, J. E. Curry, J. E. Day, P. J. Day, K. Hearn, A. Iqbal, L. Y. Lee, V. Martins P. N. Mortenson, J. M. Munck, L. W. Page, S. Patel, S. Roomans, K. Smith, E. Tamanini, G. Saxty
Fragment-Based Discovery Of Potent And Selective Ddr1/2 Inhibitors.
Acs Med. Chem. Lett. V. 6 798 2015
PubMed-ID: 26191369  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00143

(-) Compounds

Molecule 1 - EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: RESIDUES 576-894
    Gene: DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPITHELIAL DISCOIDIN DOMAIN RECEPTOR 1,CD167 ANTIGEN-LIKE FAMILY MEMBER A,CELL ADHESION KINASE,DISCOIDIN RECEPTOR TYROSINE KINASE,HGK2,MAMMARY CARCINOMA KINASE 10,MCK-10,PROTEIN-TYROSINE KINASE 3A,PROTEIN-TYROSINE KINASE RTK-6,TRK E,TYROSINE KINASE DDR, TYROSINE-PROTEIN KINASE CAK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
14VD1Ligand/IonN-[5-({[(3-FLUOROPHENYL)CARBAMOYL]AMINO}METHYL)-2-METHYLPHENYL]IMIDAZO[1,2-A]PYRIDINE-3-CARBOXAMIDE
2IOD1Ligand/IonIODIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:847binding site for residue IOD A 1001
2AC2SOFTWAREVAL A:624 , ALA A:653 , LYS A:655 , GLU A:672 , MET A:676 , LEU A:679 , ILE A:685 , THR A:701 , ASP A:702 , TYR A:703 , MET A:704 , PHE A:762 , LEU A:773 , ALA A:783 , ASP A:784 , HOH A:1176 , HOH A:1178binding site for residue 4VD A 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:604 -Phe A:605
2Asp A:695 -Pro A:696
3Glu A:776 -Asn A:777

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BVN)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeee......eeeeee.....eeeeee.....hhhhhhhhhhhhhhhhh........eeeee......eeeee....eehhhhhhhhee....eehhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee......hhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.............hhhhhhhhhhh...hhhhh.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bvn A 604 DFPRSRLRFKEKLGEGQFGEVHLCEVDSHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALN 911
                                   613       623       649       659       669       679       689       699       709       719 ||    743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903        
                                                     631|                                                                      721|                                                                                                                                                                               
                                                      648                                                                       736
   Legend:   → Mismatch (orange background)
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    → 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 5BVN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:604 - Phe A:605   [ RasMol ]  
    Asp A:695 - Pro A:696   [ RasMol ]  
    Glu A:776 - Asn A:777   [ RasMol ]  
 

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  DDR1_HUMAN | Q08345
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 Related Entries

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

UniProtKB/Swiss-Prot
        DDR1_HUMAN | Q08345: 3zos 4ag4 4bkj 4ckr 5bvk 5bvo 5bvw 5fdp 5fdx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5BVN)