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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CATHEPSIN S BOUND TO A NON-COVALENT INHIBITOR
 
Authors :  Y. Wang, P. K. Jadhav, G. G. Deng
Date :  24 Mar 14  (Deposition) - 29 Oct 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Cysteine Protease, Cathepsin S, Inhibitor, Non-Covalent (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. K. Jadhav, M. A. Schiffler, K. Gavardinas, E. J. Kim, D. P. Matthews, M. A. Staszak, D. S. Coffey, B. W. Shaw, K. C. Cassidy, R. A. Brier, Y. Zhang, R. M. Christie, W. F. Matter, K. Qing, J. D. Durbin, Y. Wang, G. G. Deng
Discovery Of Cathepsin S Inhibitor Ly3000328 For The Treatment Of Abdominal Aortic Aneurysm.
Acs Med. Chem. Lett. V. 5 1138 2014
PubMed-ID: 25313327  |  Reference-DOI: 10.1021/ML500283G

(-) Compounds

Molecule 1 - CATHEPSIN S
    Chains: A, B
    EC Number: 3.4.22.27
    Engineered: YES
    Expression System: ENTEROBACTERIA PHAGE L1
    Expression System Taxid: 268588
    Gene: CTSS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
12FC2Ligand/IonN-[(8R)-8-(BENZOYLAMINO)-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL]-4-METHYLPIPERAZINE-1-CARBOXAMIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
12FC1Ligand/IonN-[(8R)-8-(BENZOYLAMINO)-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL]-4-METHYLPIPERAZINE-1-CARBOXAMIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12FC1Ligand/IonN-[(8R)-8-(BENZOYLAMINO)-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL]-4-METHYLPIPERAZINE-1-CARBOXAMIDE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
12FC1Ligand/IonN-[(8R)-8-(BENZOYLAMINO)-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL]-4-METHYLPIPERAZINE-1-CARBOXAMIDE
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:18 , GLY A:20 , SER A:21 , HOH A:530 , LYS B:10binding site for residue SO4 A 301
2AC2SOFTWAREGLY A:62 , GLY A:68 , GLY A:69 , PHE A:70 , MET A:71 , ASN A:163 , GLY A:165 , PHE A:211 , HOH A:469 , HOH A:578 , HOH A:593 , PHE B:70 , THR B:72 , 2FC B:301binding site for residue 2FC A 302
3AC3SOFTWAREPHE A:70 , THR A:72 , GLU A:115 , 2FC A:302 , GLY B:62 , ASN B:67 , GLY B:68 , GLY B:69 , PHE B:70 , MET B:71 , GLU B:115 , ASN B:163 , GLY B:165 , PHE B:211 , HOH B:451 , HOH B:592binding site for residue 2FC B 301

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:22 -A:66
2A:56 -A:99
3A:158 -A:206
4B:22 -B:66
5B:56 -B:99
6B:158 -B:206

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P6E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P6E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P6E)

(-) Exons   (0, 0)

(no "Exon" information available for 4P6E)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhh.ee................hhh.eee...eeee....hhhhhhhhhhhh..eeeee...hhhhhh................eeeeeeeeeee..eeeeeee...........eeeee....hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p6e A   0 ILPDSVDWREKGCVTEVKYQGSCGACWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEIE 218
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         


Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhh.ee................hhh.eee...eeee....hhhhhhhhhhhh..eeeee...hhhhhh....ee..........eeeeeeeeeee..eeeeeee...........eeeee....hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p6e B   0 ILPDSVDWREKGCVTEVKYQGSCGACWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEIE 218
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
   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 4P6E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P6E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P6E)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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  4p6e
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  CATS_HUMAN | P25774
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  3.4.22.27
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CATS_HUMAN | P25774: 1bxf 1glo 1ms6 1npz 1nqc 2c0y 2f1g 2fq9 2fra 2frq 2ft2 2fud 2fye 2g6d 2g7y 2h7j 2hh5 2hhn 2hxz 2op3 2r9m 2r9n 2r9o 3iej 3kwn 3mpe 3mpf 3n3g 3n4c 3ovx 4p6g

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4P6E)