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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) - 02 Nov 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
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, M. Tawada, S. Suzuki, M. Tomimoto, M. Kondo, N. Tarui, T. Sanada, R. Kanagawa, G. Snell, C. A. Behnke, K. Kubo, T. Kuroita
Structure-Based Design Of A New Series Of N-(Piperidin-3-Yl)Pyrimidine-5-Carboxamides As Renin Inhibitors.
Bioorg. Med. Chem. V. 24 5771 2016
PubMed-ID: 27687967  |  Reference-DOI: 10.1016/J.BMC.2016.09.030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RENIN
    ChainsA, B
    EC Number3.4.23.15
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK 293
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentUNP RESIDUES 70-406
    GeneREN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymANGIOTENSINOGENASE

 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  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
16VR2Ligand/Ion2-~{TERT}-BUTYL-4-(FURAN-2-YLMETHYLAMINO)-~{N}-(2-METHYLPROPYL)-~{N}-[(3~{S})-PIPERIDIN-3-YL]PYRIMIDINE-5-CARBOXAMIDE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
16VR1Ligand/Ion2-~{TERT}-BUTYL-4-(FURAN-2-YLMETHYLAMINO)-~{N}-(2-METHYLPROPYL)-~{N}-[(3~{S})-PIPERIDIN-3-YL]PYRIMIDINE-5-CARBOXAMIDE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
16VR1Ligand/Ion2-~{TERT}-BUTYL-4-(FURAN-2-YLMETHYLAMINO)-~{N}-(2-METHYLPROPYL)-~{N}-[(3~{S})-PIPERIDIN-3-YL]PYRIMIDINE-5-CARBOXAMIDE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (3, 15)
No.NameCountTypeFull Name
16VR6Ligand/Ion2-~{TERT}-BUTYL-4-(FURAN-2-YLMETHYLAMINO)-~{N}-(2-METHYLPROPYL)-~{N}-[(3~{S})-PIPERIDIN-3-YL]PYRIMIDINE-5-CARBOXAMIDE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:18 , GLN A:19 , TYR A:20 , VAL A:36 , ASP A:38 , GLY A:40 , THR A:85 , PRO A:118 , ASP A:226 , THR A:227 , GLY A:228 , ALA A:229 , SER A:230binding site for residue 6VR A 402
2AC2SOFTWARETHR B:18 , GLN B:19 , TYR B:20 , VAL B:36 , ASP B:38 , GLY B:40 , PRO B:118 , ASP B:226 , THR B:227 , GLY B:228 , ALA B:229 , SER B:230 , HOH B:516binding site for residue 6VR B 402
3AC3SOFTWAREHIS A:74 , LEU B:195 , ARG B:330 , ASN B:331 , ASN B:332 , HOH B:514binding site for residue PEG B 403
4AC4SOFTWAREASN A:75 , HOH A:503 , HOH A:507binding site for Mono-Saccharide NAG A 401 bound to ASN A 75
5AC5SOFTWAREASN B:75 , MET B:107binding 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 5KOQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KOQ)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               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.hhhhhhhhhh.....eeeeee...........eeeee.......eeeeeeeee.......eeeeeeeee..eee....eeeee......eeehhhhhhhhhhhhh.ee....eeee.hhhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5koq A   5 NTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 340
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204      |215       225       235       245       255       265       275       285       295       305       315       325       335     
                                                                                                                                                                                                                                        211|                                                                                                                               
                                                                                                                                                                                                                                         213                                                                                                                               

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.......hhhhhh....hhhhh...eeeeeeeee..eeeeeeeeeeee..eeeeeeeeeeee.hhhhhh.....eeee..hhhhhhhhh.hhhhhhhhhh.....eeeeee...........eeeee...hhh.eeeeeeeee.......eeee..eee..eeee....eeeee......eeehhhhhhhhhhhhh.ee....eeee..hhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5koq B   4 GNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 340
                                    13        23        33        43        53        63        73        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337   
                                                                                                         82|                                                                                                                                                                                                                                                             
                                                                                                          87                                                                                                                                                                                                                                                             

   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 5KOQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 | P007971bbs 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 5kos 5kot 5sxn 5sy2 5sy3 5sz9 5t4s

(-) Related Entries Specified in the PDB File

5kos 5kot