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(-) Description

Title :  TARGETING THE PEX14-PEX5 INTERACTION BY SMALL MOLECULES PROVIDES NOVEL THERAPEUTIC ROUTES TO TREAT TRYPANOSOMIASES.
 
Authors :  M. Dawidowski, L. Emmanouilidis, M. Sattler, G. M. Popowicz
Date :  07 Jun 16  (Deposition) - 08 Mar 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Trypanosomiasis, Glycosome, Protein-Protein Interaction Inhibitor, Structure-Based Drug Discovery, Inhibitor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Dawidowski, L. Emmanouilidis, V. C. Kalel, K. Tripsianes, K. Schorpp, K. Hadian, M. Kaiser, P. Maser, M. Kolonko, S. Tanghe, A. Rodriguez, W. Schliebs, R. Erdmann, M. Sattler, G. M. Popowicz
Inhibitors Of Pex14 Disrupt Protein Import Into Glycosomes And Kill Trypanosoma Parasites.
Science V. 355 1416 2017
PubMed-ID: 28360328  |  Reference-DOI: 10.1126/SCIENCE.AAL1807

(-) Compounds

Molecule 1 - PEROXIN 14
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PEX14
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 5702

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
16RB4Ligand/Ion1-(2-HYDROXYETHYL)-5-[(4-METHOXYNAPHTHALEN-1-YL)METHYL]-~{N}-(PHENYLMETHYL)-6,7-DIHYDRO-4~{H}-PYRAZOLO[4,3-C]PYRIDINE-3-CARBOXAMIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GLY1Mod. Amino AcidGLYCINE
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
16RB1Ligand/Ion1-(2-HYDROXYETHYL)-5-[(4-METHOXYNAPHTHALEN-1-YL)METHYL]-~{N}-(PHENYLMETHYL)-6,7-DIHYDRO-4~{H}-PYRAZOLO[4,3-C]PYRIDINE-3-CARBOXAMIDE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3GLY1Mod. Amino AcidGLYCINE
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16RB1Ligand/Ion1-(2-HYDROXYETHYL)-5-[(4-METHOXYNAPHTHALEN-1-YL)METHYL]-~{N}-(PHENYLMETHYL)-6,7-DIHYDRO-4~{H}-PYRAZOLO[4,3-C]PYRIDINE-3-CARBOXAMIDE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3GLY-1Mod. Amino AcidGLYCINE
4NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
16RB1Ligand/Ion1-(2-HYDROXYETHYL)-5-[(4-METHOXYNAPHTHALEN-1-YL)METHYL]-~{N}-(PHENYLMETHYL)-6,7-DIHYDRO-4~{H}-PYRAZOLO[4,3-C]PYRIDINE-3-CARBOXAMIDE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3GLY-1Mod. Amino AcidGLYCINE
4NA-1Ligand/IonSODIUM ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
16RB1Ligand/Ion1-(2-HYDROXYETHYL)-5-[(4-METHOXYNAPHTHALEN-1-YL)METHYL]-~{N}-(PHENYLMETHYL)-6,7-DIHYDRO-4~{H}-PYRAZOLO[4,3-C]PYRIDINE-3-CARBOXAMIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GLY-1Mod. Amino AcidGLYCINE
4NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:13 , GLU A:16 , PHE A:17 , ARG A:22 , THR A:26 , PHE A:34 , LEU A:35 , HOH A:231 , HIS B:33 , 6RB B:101binding site for residue 6RB A 101
2AC2SOFTWAREPRO A:27 , THR A:28 , SER A:29 , HOH A:201 , HOH A:206 , HOH A:233 , THR C:28 , LYS C:56binding site for residue GLY A 102
3AC3SOFTWAREHIS A:33 , PHE A:34 , 6RB A:101 , ASN B:13 , PHE B:17 , ARG B:22 , THR B:26 , PHE B:34 , LYS B:38 , HOH B:215binding site for residue 6RB B 101
4AC4SOFTWAREASN C:13 , GLU C:16 , PHE C:17 , ARG C:22 , THR C:26 , SER C:30 , PHE C:34 , LEU C:35 , LYS C:38 , HOH C:224 , HIS D:33 , 6RB D:101binding site for residue 6RB C 101
5AC5SOFTWARESER C:29 , SER C:30 , HOH C:233 , HOH C:241 , HOH D:202binding site for residue NA C 102
6AC6SOFTWARESER C:30 , HIS C:33 , 6RB C:101 , ASN D:13 , GLU D:16 , PHE D:17 , ASP D:20 , ARG D:22 , THR D:26 , SER D:30 , PHE D:34 , LEU D:35 , LYS D:38 , HOH D:230binding site for residue 6RB D 101
7AC7SOFTWARELYS D:36 , LEU D:40 , SER D:41 , ALA D:42 , HOH D:208binding site for residue EDO D 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L8A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L8A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L8A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L8A)

(-) Exons   (0, 0)

(no "Exon" information available for 5L8A)

(-) 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:62
                                                                                             
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  5l8a A  5 SEREKRVSNAVEFLLDSRVRRTPTSSKVHFLKSKGLSAEEICEAFTKVGQPKTLNEIKRILS 66
                                    14        24        34        44        54        64  


Chain B from PDB  Type:PROTEIN  Length:62
                                                                                             
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  5l8a B  5 SEREKRVSNAVEFLLDSRVRRTPTSSKVHFLKSKGLSAEEICEAFTKVGQPKTLNEIKRILS 66
                                    14        24        34        44        54        64  


Chain C from PDB  Type:PROTEIN  Length:62
                                                                                             
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  5l8a C  5 SEREKRVSNAVEFLLDSRVRRTPTSSKVHFLKSKGLSAEEICEAFTKVGQPKTLNEIKRILS 66
                                    14        24        34        44        54        64  


Chain D from PDB  Type:PROTEIN  Length:62
                                                                                             
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  5l8a D  5 SEREKRVSNAVEFLLDSRVRRTPTSSKVHFLKSKGLSAEEICEAFTKVGQPKTLNEIKRILS 66
                                    14        24        34        44        54        64
   Legend:   → Mismatch (orange background)
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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 5L8A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L8A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L8A)

(-) Gene Ontology  (5, 5)

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2w84 HUMAN ORTHOLOG