5SY3 - JenaLib

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Title :   STRUCTURE-BASED DESIGN OF A NEW SERIES OF N-PIPERIDIN-3-YLPYRIMIDINE-5-CARBOXAMIDES AS RENIN INHIBITORS

Authors :   G. P. Snell, C. A. Behnke, K. Okada, O. Hideyuki, B. C. Sang, W. Lane

Date :   10 Aug 16 (Deposition) - 02 Nov 16 (Release) - 09 Nov 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A  (3x)

Keywords :   Protein-Ligand 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

Molecule 1 - RENIN
	Chains	:	A, B
	EC Number	:	3.4.23.15
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Gene	:	REN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ANGIOTENSINOGENASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 20)

No.	Name	Count	Type	Full Name
1	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
2	74Z	1	Ligand/Ion	N-[(FURAN-2-YL)METHYL]-5,6,7,8-TETRAHYDRO[1]BENZOTHIENO[2,3-D]PYRIMIDIN-4-AMINE
3	DMS	12	Ligand/Ion	DIMETHYL SULFOXIDE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (5, 10)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	74Z	1	Ligand/Ion	N-[(FURAN-2-YL)METHYL]-5,6,7,8-TETRAHYDRO[1]BENZOTHIENO[2,3-D]PYRIMIDIN-4-AMINE
3	DMS	6	Ligand/Ion	DIMETHYL SULFOXIDE
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (4, 10)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	74Z	-1	Ligand/Ion	N-[(FURAN-2-YL)METHYL]-5,6,7,8-TETRAHYDRO[1]BENZOTHIENO[2,3-D]PYRIMIDIN-4-AMINE
3	DMS	6	Ligand/Ion	DIMETHYL SULFOXIDE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 3 (5, 30)

No.	Name	Count	Type	Full Name
1	1PE	3	Ligand/Ion	PENTAETHYLENE GLYCOL
2	74Z	3	Ligand/Ion	N-[(FURAN-2-YL)METHYL]-5,6,7,8-TETRAHYDRO[1]BENZOTHIENO[2,3-D]PYRIMIDIN-4-AMINE
3	DMS	18	Ligand/Ion	DIMETHYL SULFOXIDE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:18 , TYR A:20 , VAL A:36 , TYR A:83 , PHE A:119 , PHE A:124 , THR A:227 , GLY A:228 , ALA A:229 , SER A:230 , DMS A:404 , DMS A:405	binding site for residue 74Z A 402
02	AC2	SOFTWARE	GLU A:155 , VAL A:157 , ASP A:328 , ASN A:331 , HOH A:542 , SER B:70 , SER B:71 , TYR B:72 , LYS B:73	binding site for residue DMS A 403
03	AC3	SOFTWARE	THR A:18 , GLN A:19 , SER A:230 , TYR A:231 , ASN A:260 , SER A:292 , 74Z A:402 , HOH A:638	binding site for residue DMS A 404
04	AC4	SOFTWARE	ALA A:229 , SER A:230 , 74Z A:402 , HOH A:585	binding site for residue DMS A 405
05	AC5	SOFTWARE	PRO A:30 , GLN A:31 , THR A:32 , LYS A:62 , SER B:269 , THR B:278	binding site for residue DMS A 406
06	AC6	SOFTWARE	TYR A:15 , GLU A:123 , TYR A:290 , ASN B:260	binding site for residue DMS A 407
07	AC7	SOFTWARE	SER A:209 , SER A:212 , ASP A:267 , SER A:269	binding site for residue PEG A 408
08	AC8	SOFTWARE	LEU A:195 , ILE A:196 , LYS A:197 , ARG A:329 , ARG A:330 , ASN A:331 , ASN A:332 , HOH A:601 , HIS B:74	binding site for residue 1PE A 409
09	AC9	SOFTWARE	VAL A:10 , ILE A:11 , HOH A:527	binding site for residue DMS A 410
10	AD1	SOFTWARE	ASP B:38 , THR B:85 , PRO B:118 , PHE B:119 , LEU B:121 , PHE B:124 , VAL B:127 , GLY B:228 , DMS B:405 , HOH B:530 , HOH B:617	binding site for residue 1PE B 403
11	AD2	SOFTWARE	GLU A:113 , ASN B:332	binding site for residue PEG B 404
12	AD3	SOFTWARE	THR B:18 , GLN B:19 , TYR B:20 , VAL B:36 , THR B:227 , GLY B:228 , ALA B:229 , 1PE B:403	binding site for residue DMS B 405
13	AD4	SOFTWARE	ALA B:282 , ASP B:283 , VAL B:285 , PHE B:286 , ARG B:321 , HOH B:569	binding site for residue DMS B 406
14	AD5	SOFTWARE	TYR B:60 , MET B:120 , ALA B:122 , LEU B:252	binding site for residue DMS B 407
15	AD6	SOFTWARE	LYS B:250 , ARG B:251 , PHE B:253 , ASP B:254 , TYR B:255 , HIS B:301 , ALA B:302	binding site for residue DMS B 408
16	AD7	SOFTWARE	SER B:89 , GLY B:90 , PHE B:91 , THR B:112	binding site for residue DMS B 409
17	AD8	SOFTWARE	LEU B:81 , ARG B:82 , ILE B:137 , HOH B:624	binding site for residue DMS B 410
18	AD9	SOFTWARE	ASN A:75 , MET A:107 , GLY A:138	binding site for Mono-Saccharide NAG A 401 bound to ASN A 75
19	AE1	SOFTWARE	GLU A:218 , ASN B:75 , HOH B:503 , HOH B:547 , HOH B:567 , HOH B:630	binding site for Poly-Saccharide residues NAG B 401 through NAG B 402 bound to ASN B 75

Asymmetric Unit

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

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 5SY3)

(no "PROSITE Motif" information available for 5SY3)

(no "Exon" information available for 5SY3)

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:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee...eeeeeeee....eeeeeeee.....eeee.......hhhhh.....hhhhh...eeeeeeeeee....eeeeeeeeeeeee..eeeeeeeeeeee.hhhhhh.....eeee..hhhhhhhhh.hhhhhhhhhh.....eeeeee.......eeeee...hhh.eeeeeeeee.......eeee..eee..eeee....eeeee......eeehhhhhhhhhhhhh.eee..eeeee.hhhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5sy3 A   4 GNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 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   
                                                                                                                                                                                           165|                                                                                                                                                                          
                                                                                                                                                                                            170

Chain B 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...eeeeeeeeee....eeeeeeeeeeeee..eeeeeeeeeeee.hhhhhh.....eeee..hhhhhhhhh.hhhhhhhhh......eeeeee.........eeeee...hhh.eeeeeeeee.......eeee..eee........eeeee......eeehhhhhhhhhhhhh.ee....eeee.hhhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5sy3 B   2 TLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR 340
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      |173       183       193       203       215       225       235       245       255       265       275       285       295       305       315       325       335     
                                                                                                                                                                                                168|                                     211|                                                                                                                              
                                                                                                                                                                                                 171                                      214

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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 '\|'

(no "SCOP Domain" information available for 5SY3)

(no "CATH Domain" information available for 5SY3)

(no "Pfam Domain" information available for 5SY3)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		1PE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		74Z	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Gly A:310 - Pro A:311	[ RasMol ]
		Gly B:310 - Pro B:311	[ RasMol ]
		Leu A:117 - Pro A:118	[ RasMol ]
		Leu B:117 - Pro B:118	[ RasMol ]
		Pro A:307 - Pro A:308	[ RasMol ]
		Pro B:307 - Pro B:308	[ RasMol ]
		Thr A:28 - Pro A:29	[ RasMol ]
		Thr B:28 - Pro B:29	[ RasMol ]

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	5sy3
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	3.4.23.15
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 20)

Sites (19, 19)

SS Bonds (6, 6)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (34, 34)

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