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(-) Description

Title :  STRUCTURE OF DDR1 RECEPTOR TYROSINE KINASE IN COMPLEX WITH D2099 INHIBITOR AT 2.25 ANGSTROMS RESOLUTION.
 
Authors :  S. G. Bartual, D. M. Pinkas, Z. Wang, K. Ding, P. Mahajan, K. Kupinska, S. Mukhopadhyay, C. Strain-Damerell, O. Borkowska, R. Talon, J. Kope E. Williams, C. Tallant, A. Chaikuad, F. Sorell, J. Newman, N. Burgess C. H. Arrowsmith, F. Von Delft, A. M. Edwards, C. Bountra, A. Bullock, Structural Genomics Consortium (Sgc)
Date :  16 Dec 15  (Deposition) - 08 Jun 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Ddr1 Kinase, Inhibitors, Structural Genomics, Psi- Biology, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Wang, H. Bian, S. G. Bartual, W. Du, J. Luo, H. Zhao, S. Zhang, C. Mo, Y. Zhou, Y. Xu, Z. Tu, X. Ren, X. Lu, R. A. Brekken, L. Yao, A. N. Bullock, J. Su, K. Ding
Structure-Based Design Of Tetrahydroisoquinoline-7-Carboxamides As Selective Discoidi Domain Receptor 1 (Ddr1) Inhibitors.
J. Med. Chem. V. 59 5911 2016
PubMed-ID: 27219676  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00140

(-) 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: UNP RESIDUES 601-903
    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  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
15WR1Ligand/Ion(4~{S})-4-METHYL-~{N}-[3-[(4-METHYLPIPERAZIN-1-YL)METHYL]-5-(TRIFLUOROMETHYL)PHENYL]-2-PYRIMIDIN-5-YL-3,4-DIHYDRO-1~{H}-ISOQUINOLINE-7-CARBOXAMIDE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:653 , LYS A:655 , GLU A:672 , MET A:676 , LEU A:679 , ILE A:685 , MET A:699 , THR A:701 , ASP A:702 , TYR A:703 , MET A:704 , PHE A:762 , HIS A:764 , ALA A:783 , ASP A:784 , HOH A:1190binding site for residue 5WR A 1001
2AC2SOFTWAREASN A:710 , ALA A:768 , THR A:769 , ARG A:770 , ASP A:795 , TRP A:809 , GLU A:835 , ALA A:842binding site for residue PEG A 1002
3AC3SOFTWAREMET A:817 , GLY A:818 , ARG A:841binding site for residue EDO A 1003
4AC4SOFTWAREHIS A:745 , ALA A:748 , HIS A:902 , HOH A:1110binding site for residue EDO A 1004
5AC5SOFTWAREARG A:890 , SER A:892binding site for residue EDO A 1005
6AC6SOFTWARETRP A:827 , PHE A:845 , TYR A:869 , LEU A:870 , TRP A:888binding site for residue EDO A 1006
7AC7SOFTWAREALA A:758 , THR A:759 , PRO A:897 , PHE A:898binding site for residue EDO A 1007

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:695 -Pro A:696

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FDP)

(-) 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:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhheeeeeeee...eeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhh.ee.......eehhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee......hhhhhhhhee.....eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.............hhhhhhhhhhh...hhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fdp A 604 DFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAGPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNT 912
                                   613       623       633||     656       666       676       686       696       706       716      |737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907     
                                                        634|                                                                        723|                                                                                                                                                                                 
                                                         648                                                                         735
   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 5FDP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:695 - Pro A:696   [ RasMol ]  
 

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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 5bvn 5bvo 5bvw 5fdx

(-) Related Entries Specified in the PDB File

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