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(-) Description

Title :  STRUCTURE OF CATHEPSIN D WITH INHIBITOR 2-(3,4-DIMETHOXYPHENYL)-N-[N-(4-METHYLBENZYL)CARBAMIMIDOYL]ACETAMIDE
 
Authors :  U. Graedler, P. Czodrowski, C. Tsaklakidis, M. Klein, K. Maskos, B. Leu
Date :  08 Jan 14  (Deposition) - 13 Aug 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Lysosomal Aspartic Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Gradler, P. Czodrowski, C. Tsaklakidis, M. Klein, D. Werkmann, S. Lindemann, K. Maskos, B. Leuthner
Structure-Based Optimization Of Non-Peptidic Cathepsin D Inhibitors.
Bioorg. Med. Chem. Lett. V. 24 4141 2014
PubMed-ID: 25086681  |  Reference-DOI: 10.1016/J.BMCL.2014.07.054

(-) Compounds

Molecule 1 - CATHEPSIN D LIGHT CHAIN
    Chains: A, C
    EC Number: 3.4.23.5
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: CPSD, CTSD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - CATHEPSIN D HEAVY CHAIN
    Chains: B, D
    EC Number: 3.4.23.5
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: CPSD, CTSD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
12S41Ligand/Ion2-(3,4-DIMETHOXYPHENYL)-N-[N-(4-METHYLBENZYL)CARBAMIMIDOYL]ACETAMIDE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
12S4-1Ligand/Ion2-(3,4-DIMETHOXYPHENYL)-N-[N-(4-METHYLBENZYL)CARBAMIMIDOYL]ACETAMIDE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:70 , THR A:72 , VAL B:114BINDING SITE FOR RESIDUE NAG A 400
2AC2SOFTWAREASP A:33 , TYR A:78 , SER A:80 , PHE B:131 , ILE B:134 , TYR B:205 , ILE B:229 , ASP B:231 , GLY B:233 , THR B:234BINDING SITE FOR RESIDUE 2S4 B 401
3AC3SOFTWAREASN C:70 , THR C:72 , NAG C:401 , VAL D:114BINDING SITE FOR RESIDUE NAG C 400
4AC4SOFTWARENAG C:400 , ASN D:145BINDING SITE FOR RESIDUE NAG C 401

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:27 -A:96
2A:46 -A:53
3B:222 -B:226
4B:265 -B:302
5C:27 -C:96
6C:46 -C:53
7D:222 -D:226
8D:265 -D:302

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Thr A:23 -Pro A:24
2Val A:94 -Pro A:95
3Asp B:172 -Pro B:173
4Gln B:176 -Pro B:177
5Pro B:313 -Pro B:314
6Gly B:316 -Pro B:317
7Thr C:23 -Pro C:24
8Val C:94 -Pro C:95
9Gln D:176 -Pro D:177
10Pro D:313 -Pro D:314
11Gly D:316 -Pro D:317

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OBZ)

(-) 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:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eeeeeeee....eeeeeeee.....eeee........hhhhhh...hhhhh...eeeeeeeeee....eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4obz A   2 PIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQS  98
                                    11        21        31        41        51        61        71        81        91       


Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeee...hhhhhh...eeee..hhhhhhhhh.hhhhhhhhh......eeeeee.........eeeee...hhh.eeeeeeeee.......eeeeeeeee....ee....eeeee......eeehhhhhhhhhhhh..eeee..eeeehhhhh.....eeeee..eeeee.....eeeeee..eeeeee.eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4obz B 107 GVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAA 346
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346


Chain C from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee...eeeeeeee....eeeeeeee.....eeee........hhhhhh...hhhhh...eeeeeeeeee....eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4obz C  -4 PAVTEGPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQS  98
                                     5        15        25        35        45        55        65        75        85        95   


Chain D from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee...hhhhhh...eeee..hhhhhhhhh.hhhhhhhhh......eeeeee.........eeeee...hhh.eeeeeeeee.......eeeeeeeee....ee....eeeee......eeehhhhhhhhhhhh..ee.....eeehhhhh.....eeeee..eeeee.....eeee..eeee.eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4obz D 106 GGVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAA 346
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295|      309       319       329       339       
                                                                                                                                                                                                                       295|                                              
                                                                                                                                                                                                                        300
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  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 4OBZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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        CATD_HUMAN | P07339: 1lya 1lyb 1lyw 4oc6 4od9

(-) Related Entries Specified in the PDB File

1lya 4oc6 4od9