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(-) Description

Title :  STRUCTURE OF CATHEPSIN D WITH INHIBITOR N-(3,4-DIMETHOXYBENZYL)-NALPHA-{N-[(3,4-DIMETHOXYPHENYL)ACETYL]CARBAMIMIDOYL}-D-PHENYLALANINAMIDE
 
Authors :  U. Graedler, P. Czodrowski, C. Tsaklakidis, M. Klein, K. Maskos, B. Leu
Date :  10 Jan 14  (Deposition) - 13 Aug 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
12RZ2Ligand/IonN-(3,4-DIMETHOXYBENZYL)-NALPHA-{N-[(3,4-DIMETHOXYPHENYL)ACETYL]CARBAMIMIDOYL}-D-PHENYLALANINAMIDE
2ACT2Ligand/IonACETATE ION
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
12RZ1Ligand/IonN-(3,4-DIMETHOXYBENZYL)-NALPHA-{N-[(3,4-DIMETHOXYPHENYL)ACETYL]CARBAMIMIDOYL}-D-PHENYLALANINAMIDE
2ACT1Ligand/IonACETATE ION
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:70 , THR A:72 , NAG A:102 , ASN B:145 , VAL B:147BINDING SITE FOR RESIDUE NAG A 101
2AC2SOFTWARENAG A:101 , ASN B:145BINDING SITE FOR RESIDUE NAG A 102
3AC3SOFTWAREALA A:13 , ASP A:33 , GLY A:35 , TYR A:78 , GLY A:79 , SER A:80 , HOH A:236 , THR B:125 , PHE B:126 , PHE B:131 , ILE B:134 , TYR B:205 , ILE B:229 , ASP B:231 , GLY B:233 , THR B:234 , MET B:309 , ILE B:311 , ACT B:402BINDING SITE FOR RESIDUE 2RZ A 103
4AC4SOFTWAREASN B:199BINDING SITE FOR RESIDUE NAG B 401
5AC5SOFTWARE2RZ A:103 , GLY B:233 , THR B:234 , SER B:235 , HOH B:513BINDING SITE FOR RESIDUE ACT B 402
6AC6SOFTWAREASN C:70 , THR C:72 , NAG C:401 , HOH C:553 , HOH C:569BINDING SITE FOR RESIDUE NAG C 400
7AC7SOFTWARENAG C:400 , ASN D:145BINDING SITE FOR RESIDUE NAG C 401
8AC8SOFTWAREGLY D:233 , THR D:234 , SER D:235 , 2RZ D:402 , HOH D:525BINDING SITE FOR RESIDUE ACT D 401
9AC9SOFTWAREALA C:13 , ASP C:33 , GLY C:35 , TYR C:78 , GLY C:79 , SER C:80 , THR D:125 , PHE D:131 , ILE D:134 , TYR D:205 , ILE D:229 , ASP D:231 , GLY D:233 , THR D:234 , MET D:309 , ASP D:310 , ACT D:401BINDING SITE FOR RESIDUE 2RZ D 402

(-) 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  (10, 10)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OD9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OD9)

(-) Exons   (0, 0)

(no "Exon" information available for 4OD9)

(-) 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
                 4od9 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.......eeee.eeee....ee....eeeee......eeehhhhhhhhhhhh..ee.....eeehhhhhhhh..eeeee..eeeeehhhhheeeeee..eeeeee.eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4od9 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: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
                 4od9 C   2 PIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQS  98
                                    11        21        31        41        51        61        71        81        91       


Chain D from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee............eeee..hhhhhhhhh.hhhhhhhhh......eeeeee.........eeeee...hhh.eeeeeeeee.......eeee.eeee....ee....eeeee......eeehhhhhhhhhhhh..ee.....eeehhhhhhhh..eeeee..eeeeehhhhheeeee....eeeee.eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4od9 D 106 GGVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAA 346
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345
   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 4OD9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OD9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OD9)

(-) Gene Ontology  (19, 19)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

1lya 4obz 4oc6