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(-) Description

Title :  STRUCTURE OF DDR1 RECEPTOR TYROSINE KINASE IN COMPLEX WITH D2164 INHIBITOR AT 2.65 ANGSTROMS RESOLUTION.
 
Authors :  S. G. Bartual, D. M. Pinkas, Z. Wang, K. Ding, P. Mahajan, K. Kupinska, S. Mukhopadhyay, C. Strain-Damerell, R. Chalk, O. Borkowska, R. Talo J. Kopec, E. Williams, C. Tallant, A. Chaikuad, F. Sorell, J. Newman, N Brown, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra, A. Bu Structural Genomics Consortium (Sgc)
Date :  16 Dec 15  (Deposition) - 26 Oct 16  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ddr1 Kinase, Inhibitors, Structural Genomics, Psi-Biology, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. G. Bartual, K. Ding, Z. Wang, N. A. Bullock
Structure Of Ddr1 Receptor Tyrosine Kinase In Complex With D2164 Inhibitor At 2. 65 Angstroms Resolution.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
    Chains: A, B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 601-913
    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,DDR1 RECEPTOR 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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
15X12Ligand/Ion3-[(4-METHYLPIPERAZIN-1-YL)METHYL]-~{N}-[(4~{R})-4-METHYL-2-PYRIMIDIN-5-YL-3,4-DIHYDRO-1~{H}-ISOQUINOLIN-7-YL]-5-(TRIFLUOROMETHYL)BENZAMIDE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
15X11Ligand/Ion3-[(4-METHYLPIPERAZIN-1-YL)METHYL]-~{N}-[(4~{R})-4-METHYL-2-PYRIMIDIN-5-YL-3,4-DIHYDRO-1~{H}-ISOQUINOLIN-7-YL]-5-(TRIFLUOROMETHYL)BENZAMIDE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
15X11Ligand/Ion3-[(4-METHYLPIPERAZIN-1-YL)METHYL]-~{N}-[(4~{R})-4-METHYL-2-PYRIMIDIN-5-YL-3,4-DIHYDRO-1~{H}-ISOQUINOLIN-7-YL]-5-(TRIFLUOROMETHYL)BENZAMIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:653 , LYS A:655 , GLU A:672 , MET A:676 , LEU A:679 , ILE A:684 , ILE A:685 , THR A:701 , ASP A:702 , MET A:704 , PHE A:762 , HIS A:764 , ALA A:783 , ASP A:784binding site for residue 5X1 A 1001
02AC2SOFTWARETRP A:812 , ILE A:815 , VAL A:853 , ASN A:856 , ALA A:857 , EDO A:1004binding site for residue EDO A 1002
03AC3SOFTWARESER A:714 , CYS A:840 , ARG A:841 , MET B:817binding site for residue EDO A 1003
04AC4SOFTWARETRP A:827 , TYR A:869 , LEU A:870 , TRP A:888 , EDO A:1002binding site for residue EDO A 1004
05AC5SOFTWAREHIS A:648binding site for residue EDO A 1005
06AC6SOFTWAREGLN B:900binding site for residue PEG A 1006
07AC7SOFTWAREALA B:653 , GLU B:672 , MET B:676 , LEU B:679 , ILE B:684 , ILE B:685 , MET B:699 , THR B:701 , ASP B:702 , TYR B:703 , MET B:704 , PHE B:762 , HIS B:764 , ALA B:783 , ASP B:784binding site for residue 5X1 B 1001
08AC8SOFTWAREPHE B:861binding site for residue EDO B 1002
09AC9SOFTWAREILE B:815 , TRP B:827 , PHE B:845 , LEU B:870 , TRP B:888binding site for residue PEG B 1003
10AD1SOFTWAREALA B:803 , VAL B:804binding site for residue PEG B 1004

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:691 -A:698

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asp A:695 -Pro A:696
2Arg A:798 -Val A:799
3Gln A:800 -Gly A:801
4Ser B:631 -Pro B:632
5Asp B:695 -Pro B:696

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FDX)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhheeeeeeee...eeeeeeee.........eeeeeeee....hhhhhhhhhhhhhhhh.........eeee.......eeeee.....hhhhhhhh.ee...eehhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee......hhhhhhhh..............hhhhhhh...hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.............hhhhhhhhhhhh........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fdx A 604 DFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEGPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDA 909
                                   613       623       633  ||   654       664       674       684       694       704       714    || 739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909
                                                          636|                                                                    719|                                                                                                                                                                              
                                                           648                                                                     735                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee...eeeeeee.....eeeeeee....hhhhhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhhhee......eehhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee......hhhhhhhh..............hhhhhhh...hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.............hhhhhhhhhhh...hhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fdx B 605 FPRSRLRFKEKLGEGQFGEVHLCEVDSPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAGPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAE 907
                                   614       624       651       661       671       681       691       701       711       721||     743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903    
                                                     632|                                                                     722|                                                                                                                                                                            
                                                      650                                                                      735
   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 5FDX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (44, 44)

Asymmetric Unit(hide GO term definitions)

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        DDR1_HUMAN | Q08345: 3zos 4ag4 4bkj 4ckr 5bvk 5bvn 5bvo 5bvw 5fdp

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