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(-) Description

Title :  RENIN IN COMPLEX WITH (4S)-4-ISOPROPYL-4-METHYL-6-OXO-1-(3-(2-OXO-4-PHENYLPYRROLIDIN-1-YL)BENZYL)TETRAHYDROPYRIMIDIN-2(1H)-IMINIUM
 
Authors :  P. Orth
Date :  29 Jan 15  (Deposition) - 18 Feb 15  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (3x)
Biol. Unit 4:  A  (3x)
Biol. Unit 5:  B  (3x)
Keywords :  Animals, Antihypertensive Agents, Blood Pressure, Drug Design, Enzyme Inhibitors, Models, Molecular, Protein Conformation, Renin, Structure-Activity Relationship, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Mckittrick
Iminopyrimidinones: A Novel Pharmacophore For The Development Of Orally Active Renin Inhibitors
Bioorg. Med. Chem. Lett. 2015
PubMed: search  |  Reference-DOI: 10.1016/J.BMCL.2015.02.003

(-) Compounds

Molecule 1 - RENIN
    Chains: A, B
    EC Number: 3.4.23.15
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 HEK
    Expression System Taxid: 9606
    Gene: REN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: LTLG NTTSSVILTN YMDTQYYGEI GIGTPPQTFK VVFDTGSSNV WVPSSKCSRL YTACVYHKLF DASDSSSYKH NGTELTLRYS TGTVSGFLSQ DIITVGGITV TQMFGEVTEM PALPFMLAEF DGVVGMGFIE QAIGRVTPIF DNIISQGVLK EDVFSFYYNR DSENSQSLGG QIVLGGSDPQ HYEGNFHYIN LIKTGVWQIQ MKGVSVGSST LLCEDGCLAL VDTGASYISG STSSIEKLME ALGAKKRLFD YVVKCNEGPT LPDISFHLGG KEYTLTSADY VFQESYSSKK LCTLAIHAMD IPPPTGPTWA LGATFIRKFY TEFDRRNNRI GFALAR
    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
Biological Unit 4 (3x): A 
Biological Unit 5 (3x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
170Y2Ligand/Ion(2Z,6S)-2-IMINO-6-METHYL-3-{3-[(4R)-2-OXO-4-PHENYLPYRROLIDIN-1-YL]BENZYL}-6-(PROPAN-2-YL)TETRAHYDROPYRIMIDIN-4(1H)-ONE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
170Y1Ligand/Ion(2Z,6S)-2-IMINO-6-METHYL-3-{3-[(4R)-2-OXO-4-PHENYLPYRROLIDIN-1-YL]BENZYL}-6-(PROPAN-2-YL)TETRAHYDROPYRIMIDIN-4(1H)-ONE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
170Y1Ligand/Ion(2Z,6S)-2-IMINO-6-METHYL-3-{3-[(4R)-2-OXO-4-PHENYLPYRROLIDIN-1-YL]BENZYL}-6-(PROPAN-2-YL)TETRAHYDROPYRIMIDIN-4(1H)-ONE
2NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (2, 9)
No.NameCountTypeFull Name
170Y6Ligand/Ion(2Z,6S)-2-IMINO-6-METHYL-3-{3-[(4R)-2-OXO-4-PHENYLPYRROLIDIN-1-YL]BENZYL}-6-(PROPAN-2-YL)TETRAHYDROPYRIMIDIN-4(1H)-ONE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
170Y3Ligand/Ion(2Z,6S)-2-IMINO-6-METHYL-3-{3-[(4R)-2-OXO-4-PHENYLPYRROLIDIN-1-YL]BENZYL}-6-(PROPAN-2-YL)TETRAHYDROPYRIMIDIN-4(1H)-ONE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 5 (1, 3)
No.NameCountTypeFull Name
170Y3Ligand/Ion(2Z,6S)-2-IMINO-6-METHYL-3-{3-[(4R)-2-OXO-4-PHENYLPYRROLIDIN-1-YL]BENZYL}-6-(PROPAN-2-YL)TETRAHYDROPYRIMIDIN-4(1H)-ONE
2NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:85 , ASP A:104 , TYR A:149 , SER A:150 , THR A:151 , PRO A:184 , ASP A:292 , GLY A:294 , ALA A:295 , SER A:296binding site for residue 70Y A 502
2AC2SOFTWAREASP B:104 , TYR B:149 , SER B:150 , THR B:151 , PRO B:184 , ASP B:292 , GLY B:294 , ALA B:295 , SER B:296 , MET B:369binding site for residue 70Y B 501
3AC3SOFTWAREASN A:141 , HOH A:605binding site for Mono-Saccharide NAG A 501 bound to ASN A 141

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:117 -A:124
2A:283 -A:287
3A:325 -A:362
4B:117 -B:124
5B:283 -B:287
6B:325 -B:362

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Thr A:94 -Pro A:95
2Leu A:183 -Pro A:184
3Pro A:373 -Pro A:374
4Gly A:376 -Pro A:377
5Thr B:94 -Pro B:95
6Leu B:183 -Pro B:184
7Pro B:373 -Pro B:374
8Gly B:376 -Pro B:377

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XX4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XX4)

(-) Exons   (0, 0)

(no "Exon" information available for 4XX4)

(-) 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:339
                                                                                                                                                                                                                                                                                                                                                                                   
               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...eee....eeeee......eeehhhhhhhhhhhhh.ee....eeee.hhhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xx4 A  68 TLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 406
                                    77        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       347       357       367       377       387       397         


Chain B from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               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....ee....eeeee......eeehhhhhhhhhhhhh.ee....eeee.hhhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xx4 B  67 LTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 406
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226     ||238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398        
                                                                                                                                                                                               232|                                                                                                                                                                           
                                                                                                                                                                                                235
   Legend:   → Mismatch (orange background)
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  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 4XX4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XX4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XX4)

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

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  4xx4
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  RENI_HUMAN | P00797
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  3.4.23.15
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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 5koq 5kos 5kot 5sxn 5sy2 5sy3 5sz9 5t4s

(-) Related Entries Specified in the PDB File

4xx3