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(-) Description

Title :  DISCOVERY OF TAK-272: A NOVEL, POTENT AND ORALLY ACTIVE RENIN IN-HIBITOR
 
Authors :  G. P. Snell, C. A. Behnke, K. Okada, O. Hideyuki, B. -C. Sang, W. Lane
Date :  01 Jul 16  (Deposition) - 05 Jul 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (3x)
Keywords :  Protein-Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Imaeda, H. Tokuhara, Y. Fukase, R. Kanagawa, Y. Kajimoto, K. Kusumoto, M. Kondo, G. P. Snell, C. A. Behnke, T. Kuroita
Discovery Of Tak-272: A Novel, Potent And Orally Active Renin Inhibitor
To Be Published
PubMed: search

(-) 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
    Fragment: UNP RESIDUES 70-406
    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, 24)

Asymmetric Unit (5, 24)
No.NameCountTypeFull Name
16VU2Ligand/Ion1-(4-METHOXYBUTYL)-~{N}-(2-METHYLPROPYL)-~{N}-[(3~{S},5~{R})-5-MORPHOLIN-4-YLCARBONYLPIPERIDIN-3-YL]BENZIMIDAZOLE-2-CARBOXAMIDE
2DMS14Ligand/IonDIMETHYL SULFOXIDE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (5, 14)
No.NameCountTypeFull Name
16VU1Ligand/Ion1-(4-METHOXYBUTYL)-~{N}-(2-METHYLPROPYL)-~{N}-[(3~{S},5~{R})-5-MORPHOLIN-4-YLCARBONYLPIPERIDIN-3-YL]BENZIMIDAZOLE-2-CARBOXAMIDE
2DMS8Ligand/IonDIMETHYL SULFOXIDE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (5, 10)
No.NameCountTypeFull Name
16VU1Ligand/Ion1-(4-METHOXYBUTYL)-~{N}-(2-METHYLPROPYL)-~{N}-[(3~{S},5~{R})-5-MORPHOLIN-4-YLCARBONYLPIPERIDIN-3-YL]BENZIMIDAZOLE-2-CARBOXAMIDE
2DMS6Ligand/IonDIMETHYL SULFOXIDE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 3 (5, 72)
No.NameCountTypeFull Name
16VU6Ligand/Ion1-(4-METHOXYBUTYL)-~{N}-(2-METHYLPROPYL)-~{N}-[(3~{S},5~{R})-5-MORPHOLIN-4-YLCARBONYLPIPERIDIN-3-YL]BENZIMIDAZOLE-2-CARBOXAMIDE
2DMS42Ligand/IonDIMETHYL SULFOXIDE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG12Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE6Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:18 , GLN A:19 , TYR A:20 , VAL A:36 , ASP A:38 , GLY A:40 , TYR A:83 , SER A:84 , THR A:85 , PRO A:118 , PHE A:124 , VAL A:127 , LEU A:224 , ASP A:226 , THR A:227 , GLY A:228 , SER A:230 , THR A:309 , DMS A:411 , HOH A:537binding site for residue 6VU A 402
02AC2SOFTWAREASN A:189 , HIS A:191 , LYS A:275 , GLU A:276 , TYR A:277 , PHE A:336 , DMS A:414 , HOH A:519binding site for residue PGE A 403
03AC3SOFTWARELYS A:197 , LEU B:54binding site for residue PEG A 405
04AC4SOFTWAREGLY A:211 , SER A:212 , THR A:214 , GLU A:276binding site for residue PEG A 406
05AC5SOFTWAREASP A:17 , ALA A:282 , ASP A:283 , VAL A:285 , PHE A:286 , ARG A:321binding site for residue DMS A 407
06AC6SOFTWAREVAL A:59 , TYR A:60 , SER A:84 , MET A:303 , ASP A:304binding site for residue DMS A 408
07AC7SOFTWAREARG A:251 , LEU A:252 , PHE A:253 , ASP A:254 , TYR A:255 , HIS A:301 , ALA A:302 , HOH A:615binding site for residue DMS A 409
08AC8SOFTWAREHIS A:61 , MET A:120 , ALA A:122 , LEU A:252binding site for residue DMS A 410
09AC9SOFTWARESER A:84 , ASP A:226 , MET A:303 , ALA A:314 , 6VU A:402binding site for residue DMS A 411
10AD1SOFTWARESER A:70 , TYR A:72 , LYS A:73 , GLU B:155 , VAL B:157 , ASP B:328 , HOH B:541binding site for residue DMS A 412
11AD2SOFTWARELEU A:79 , LEU A:81 , PHE A:91 , GLY A:109 , VAL A:111 , HOH A:589binding site for residue DMS A 413
12AD3SOFTWAREGLY A:188 , ASN A:189 , PGE A:403 , THR B:98 , GLY B:100binding site for residue DMS A 414
13AD4SOFTWARETHR B:18 , GLN B:19 , TYR B:20 , VAL B:36 , ASP B:38 , GLY B:40 , TYR B:83 , SER B:84 , THR B:85 , PRO B:118 , VAL B:127 , LEU B:224 , ASP B:226 , THR B:227 , GLY B:228 , ALA B:229 , SER B:230 , ILE B:305 , THR B:309 , DMS B:405 , DMS B:410 , HOH B:553binding site for residue 6VU B 402
14AD5SOFTWAREHIS A:74 , LEU B:195 , ILE B:196 , LYS B:197 , ARG B:330 , ASN B:331 , ASN B:332 , HOH B:558binding site for residue PGE B 403
15AD6SOFTWARETHR B:85 , LEU B:121 , HIS B:301 , HOH B:511binding site for residue PEG B 404
16AD7SOFTWARESER B:84 , ASP B:226 , ALA B:314 , 6VU B:402binding site for residue DMS B 405
17AD8SOFTWARETHR B:18 , GLN B:19 , SER B:230 , ASN B:260binding site for residue DMS B 406
18AD9SOFTWAREGLU B:276 , TYR B:277 , PHE B:323 , HOH B:556binding site for residue DMS B 407
19AE1SOFTWARELEU B:79 , LEU B:81 , GLY B:90 , PHE B:91 , GLY B:109 , VAL B:111 , HOH B:520binding site for residue DMS B 408
20AE2SOFTWAREGLU A:187 , ILE B:11 , HOH B:542binding site for residue DMS B 409
21AE3SOFTWARESER B:41 , ARG B:82 , ILE B:137 , 6VU B:402binding site for residue DMS B 410
22AE4SOFTWAREASN A:75 , HOH A:517 , HOH A:527binding site for Mono-Saccharide NAG A 401 bound to ASN A 75
23AE5SOFTWAREASN B:75 , THR B:77 , MET B:107 , HOH B:537 , HOH B:599binding 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 5KOT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KOT)

(-) 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:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee...eeeeeeee....eeeeeeee.....eeee.......hhhhhhh...hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeee.hhhhhh.....eeee..hhhhhhhhh.hhhhhhhhh......eeeeee......eeeee...hhh.eeeeeeeee.......eeeeeeeee..eeee....eeeee......eeehhhhhhhhhhhhh.ee....eeee.hhhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhh.eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kot A   4 GNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 340
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163  ||   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338  
                                                                                                                                                                                            166|                                                                                                                                                                        
                                                                                                                                                                                             172                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee...eeeeeeee....eeeeeeee.....eeee.......hhhhhhh...hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeee.hhhhhh.....eeee..hhhhhhhhh.hhhhhhhhh......eeeeee.......eeeee...hhh.eeeeeeeee.......eeeeeeeee..eeee....eeeee......eeehhhhhhhhhhhhh.ee....eeee.hhhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kot B   4 GNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 340
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163  ||   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337   
                                                                                                                                                                                            166|                                                                                                                                                                         
                                                                                                                                                                                             171
   Legend:   → Mismatch (orange background)
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    → 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 5KOT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

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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 5sxn 5sy2 5sy3 5sz9 5t4s

(-) Related Entries Specified in the PDB File

5koq 5kos