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(-) Description

Title :  NOVEL APPROACH OF FRAGMENT-BASED LEAD DISCOVERY APPLIED TO RENIN INHIBITORS
 
Authors :  G. P. Snell, C. A. Behnke, K. Okada, H. Oki, B. C. Sang, W. Lane
Date :  30 Aug 16  (Deposition) - 26 Oct 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (3x)
Keywords :  Protein-Ligand Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Tawada, S. Suzuki, Y. Imaeda, H. Oki, G. Snell, C. A. Behnke, M. Kondo N. Tarui, T. Tanaka, T. Kuroita, M. Tomimoto
Novel Approach Of Fragment-Based Lead Discovery Applied To Renin Inhibitors.
Bioorg. Med. Chem. V. 24 6066 2016
PubMed-ID: 27720325  |  Reference-DOI: 10.1016/J.BMC.2016.09.065

(-) Compounds

Molecule 1 - RENIN
    Chains: A, B
    EC Number: 3.4.23.15
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: REN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANGIOTENSINOGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
177O1Ligand/Ion6-CHLORO-N-[(FURAN-2-YL)METHYL]PYRAZIN-2-AMINE
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PG61Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
177O-1Ligand/Ion6-CHLORO-N-[(FURAN-2-YL)METHYL]PYRAZIN-2-AMINE
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PG61Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
5PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
177O1Ligand/Ion6-CHLORO-N-[(FURAN-2-YL)METHYL]PYRAZIN-2-AMINE
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PG6-1Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 3 (5, 21)
No.NameCountTypeFull Name
177O3Ligand/Ion6-CHLORO-N-[(FURAN-2-YL)METHYL]PYRAZIN-2-AMINE
2DMS6Ligand/IonDIMETHYL SULFOXIDE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PG63Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
5PGE3Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:83 , THR A:85 , PRO A:118 , PHE A:124 , GLY A:228binding site for residue PG6 A 402
2AC2SOFTWARETHR A:18 , GLN A:19 , TYR A:20 , VAL A:36 , THR A:227 , GLY A:228 , ALA A:229binding site for residue DMS A 403
3AC3SOFTWAREALA A:282 , ASP A:283 , VAL A:285 , PHE A:286 , ARG A:321 , HOH A:537binding site for residue DMS A 404
4AC4SOFTWARETHR B:18 , TYR B:20 , VAL B:36 , PHE B:119 , PHE B:124 , THR B:227 , GLY B:228 , ALA B:229 , SER B:230binding site for residue 77O B 402
5AC5SOFTWAREHIS A:74 , LEU B:195 , ARG B:330 , ASN B:331 , ASN B:332 , HOH B:521binding site for residue PGE B 403
6AC6SOFTWAREASN A:75 , HOH A:504 , HOH A:509 , HOH A:560binding site for Mono-Saccharide NAG A 401 bound to ASN A 75
7AC7SOFTWAREASN B:75binding site for Mono-Saccharide NAG B 401 bound to ASN B 75

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:51 -A:58
2A:217 -A:221
3A:259 -A:296
4B:51 -B:58
5B:217 -B:221
6B:259 -B:296

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Thr A:28 -Pro A:29
2Leu A:117 -Pro A:118
3Pro A:307 -Pro A:308
4Gly A:310 -Pro A:311
5Thr B:28 -Pro B:29
6Leu B:117 -Pro B:118
7Pro B:307 -Pro B:308
8Gly B:310 -Pro B:311

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T4S)

(-) Exons   (0, 0)

(no "Exon" information available for 5T4S)

(-) 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee...eeeeeeee....eeeeeeee.....eeee.......hhhhhh....hhhhh...eeeeeeeeee....eeeeeeeeeeeee..eeeeeeeeeeee.hhhhhh.....eeee..hhhhhhhhh.hhhhhhhhh......eeeeee........eeeee...hhh.eeeeeeeee.......eeee.eeee........eeeee......eeehhhhhhhhhhhhh.ee....eeee.hhh.....eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t4s A   2 TLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 340
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   ||  174       184       194       204      |216       226       236       246       256       266       276       286       296       306       316       326       336    
                                                                                                                                                                                             165|                                       211|                                                                                                                              
                                                                                                                                                                                              169                                        214                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee...eeeeeeee....eeeeeeee.....eeee.......hhhhh.....hhhhh...eeeeeeeee..eeeeeeeeeeee..eeeeeeeeeeee.hhhhhh.....eeee..hhhhh.....hhhhhhhhh......eeeeee........eeeee...hhh.eeeeeeeee.......eeee..eee..eeee....eeeee......eeehhhhhhhhhhhhh.ee....eeee.hhhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t4s B   3 LGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 340
                                    12        22        32        42        52        62        72        82|       96       106       116       126       136       146       156       166|      179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339 
                                                                                                          82|                                                                            166|                                                                                                                                                                          
                                                                                                           87                                                                             170
   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 5T4S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T4S)

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

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  5t4s
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 Related Entries

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

UniProtKB/Swiss-Prot
        RENI_HUMAN | P00797: 1bbs 1bil 1bim 1hrn 1rne 2bks 2bkt 2fs4 2g1n 2g1o 2g1r 2g1s 2g1y 2g20 2g21 2g22 2g24 2g26 2g27 2i4q 2iko 2iku 2il2 2ren 2v0z 2v10 2v11 2v12 2v13 2v16 2x0b 3d91 3g6z 3g70 3g72 3gw5 3k1w 3km4 3o9l 3oad 3oag 3oot 3oqf 3oqk 3own 3q3t 3q4b 3q5h 3sfc 3vcm 3vsw 3vsx 3vuc 3vyd 3vye 3vyf 4amt 4gj5 4gj6 4gj7 4gj8 4gj9 4gja 4gjb 4gjc 4gjd 4pyv 4q1n 4ryc 4ryg 4rz1 4s1g 4xx3 4xx4 5koq 5kos 5kot 5sxn 5sy2 5sy3 5sz9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5T4S)