4Q1N - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE-BASED DESIGN OF 4-HYDROXY-3,5-SUBSTITUTED PIPERIDINES AS DIRECT RENIN INHIBITORS

Authors :   N. Schiering, A. D'Arcy, O. Irie, F. Yokokawa

Date :   04 Apr 14 (Deposition) - 06 Aug 14 (Release) - 06 Aug 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

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

Keywords :   Aspartic Protease, Angiotensin, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Ehara, O. Irie, T. Kosaka, T. Kanazawa, W. Breitenstein, P. Grosche N. Ostermann, M. Suzuki, S. Kawakami, K. Konishi, Y. Hitomi, A. Toyao, H. Gunji, F. Cumin, N. Schiering, T. Wagner, D. F. Rigel, R. L. Webb, J. Maibaum, F. Yokokawa
Structure-Based Design Of Substituted Piperidines As A New Class Of Highly Efficacious Oral Direct Renin Inhibitors.
Acs Med Chem Lett V. 5 787 2014
PubMed-ID: 25050166 | Reference-DOI: 10.1021/ML500137B

Molecule 1 - RENIN
	Chains	:	A, B
	EC Number	:	3.4.23.15
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK
	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	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	2Y9	2	Ligand/Ion	(3S,4R,5R)-N-CYCLOPROPYL-N'-[(2R)-1-ETHOXY-4-METHYLPENTAN-2-YL]-4-HYDROXY-N-[5-(PROPAN-2-YL)PYRIDIN-2-YL]PIPERIDINE-3,5-DICARBOXAMIDE
2	DMS	3	Ligand/Ion	DIMETHYL SULFOXIDE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	2Y9	1	Ligand/Ion	(3S,4R,5R)-N-CYCLOPROPYL-N'-[(2R)-1-ETHOXY-4-METHYLPENTAN-2-YL]-4-HYDROXY-N-[5-(PROPAN-2-YL)PYRIDIN-2-YL]PIPERIDINE-3,5-DICARBOXAMIDE
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	2Y9	1	Ligand/Ion	(3S,4R,5R)-N-CYCLOPROPYL-N'-[(2R)-1-ETHOXY-4-METHYLPENTAN-2-YL]-4-HYDROXY-N-[5-(PROPAN-2-YL)PYRIDIN-2-YL]PIPERIDINE-3,5-DICARBOXAMIDE
2	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (4, 24)

No.	Name	Count	Type	Full Name
1	2Y9	6	Ligand/Ion	(3S,4R,5R)-N-CYCLOPROPYL-N'-[(2R)-1-ETHOXY-4-METHYLPENTAN-2-YL]-4-HYDROXY-N-[5-(PROPAN-2-YL)PYRIDIN-2-YL]PIPERIDINE-3,5-DICARBOXAMIDE
2	DMS	9	Ligand/Ion	DIMETHYL SULFOXIDE
3	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:12 , GLN A:13 , TYR A:14 , VAL A:30 , THR A:216 , GLY A:217 , ALA A:218	BINDING SITE FOR RESIDUE DMS A 401
2	AC2	SOFTWARE	ASN A:67 , HOH A:547 , HOH A:675 , HOH A:690 , HOH A:692	BINDING SITE FOR RESIDUE NAG A 402
3	AC3	SOFTWARE	LEU A:47A , TYR A:47B	BINDING SITE FOR RESIDUE PO4 A 403
4	AC4	SOFTWARE	ASP A:32 , GLY A:34 , ARG A:74 , TYR A:75 , SER A:76 , THR A:77 , PRO A:111 , ALA A:115 , VAL A:120 , ILE A:130 , ASP A:215 , GLY A:217 , ALA A:218 , THR A:295	BINDING SITE FOR RESIDUE 2Y9 A 404
5	AC5	SOFTWARE	THR B:12 , GLN B:13 , TYR B:14 , VAL B:30 , THR B:216 , GLY B:217 , ALA B:218	BINDING SITE FOR RESIDUE DMS B 401
6	AC6	SOFTWARE	GLY B:217 , SER B:219 , 2Y9 B:404 , HOH B:582 , HOH B:598	BINDING SITE FOR RESIDUE DMS B 402
7	AC7	SOFTWARE	ASN B:67	BINDING SITE FOR RESIDUE NAG B 403
8	AC8	SOFTWARE	ASP B:32 , GLY B:34 , ARG B:74 , TYR B:75 , SER B:76 , THR B:77 , PRO B:111 , ALA B:115 , PHE B:117 , ASP B:215 , GLY B:217 , THR B:295 , DMS B:402 , HOH B:598	BINDING SITE FOR RESIDUE 2Y9 B 404

Asymmetric Unit

No.	Residues
1	A:45	-	A:50
2	A:206	-	A:210
3	A:249	-	A:282
4	B:45	-	B:50
5	B:206	-	B:210
6	B:249	-	B:282

Asymmetric Unit

No.	Residues
1	Thr A:22	-	Pro A:23
2	Leu A:110	-	Pro A:111
3	Pro A:293	-	Pro A:294
4	Gly A:296	-	Pro A:297
5	Thr B:22	-	Pro B:23
6	Leu B:110	-	Pro B:111
7	Pro B:293	-	Pro B:294
8	Gly B:296	-	Pro B:297

(no "SAP(SNP)/Variant" information available for 4Q1N)

(no "PROSITE Motif" information available for 4Q1N)

(no "Exon" information available for 4Q1N)

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:336
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeee...eeeeeeee....eeeeeeee.....eeee.......hhhhhh....hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeee.hhhhhh.....eeee..hhhhhhhhh.hhhhhhhhh......eeeeee.......eeeee...hhh.eeeeeeeee.......eeee.eeee..eeee....eeeee......eeehhhhhhhhhhhhh.ee....eeee.hhhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4q1n A   -5 LTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR  326
                                     4        14        24        34        44   ||   52        62        72        82        92    || 103       113       123       133       143       153    |||163       173       183       193       203       213       223       233       244       254       264       274      281C|      290       300       310       320      
                                                                               47A|                                                97|                                                        158||                                                                               242|                                  281A|||                                             
                                                                                47B                                                 99                                                        160C|                                                                                244                                   281B||                                             
                                                                                                                                                                                               160D                                                                                                                       281C|                                             
                                                                                                                                                                                                                                                                                                                           281D

Chain B from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeee...eeeeeeee....eeeeeeee.....eeee........hhhhhh...hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeee.hhhhhh.....eeee..hhhhhhhhh.hhhhhhhhh......eeeeee.......eeeee...hhh.eeeeeeeee.......eeee.eeee..eeee....eeeee......eeehhhhhhhhhhhhh.ee....eeee.hhhhhh..eeeee..eeeeehhhhhh.........eee..eee..........eeehhhhhhheeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4q1n B   -5 LTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR  326
                                     4        14        24        34        44   ||   52        62        72        82        92    || 103       113       123       133       143       153    |||163       173       183       193       203       213       223       233       244       254       264       274      281C|      290       300       310       320      
                                                                               47A|                                                97|                                                        158||                                                                               242|                                  281A|||                                             
                                                                                47B                                                 99                                                        160C|                                                                                244                                   281B||                                             
                                                                                                                                                                                               160D                                                                                                                       281C|                                             
                                                                                                                                                                                                                                                                                                                           281D

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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 4Q1N)

(no "CATH Domain" information available for 4Q1N)

(no "Pfam Domain" information available for 4Q1N)

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	Cis Peptide Bonds
		Gly A:296 - Pro A:297	[ RasMol ]
		Gly B:296 - Pro B:297	[ RasMol ]
		Leu A:110 - Pro A:111	[ RasMol ]
		Leu B:110 - Pro B:111	[ RasMol ]
		Pro A:293 - Pro A:294	[ RasMol ]
		Pro B:293 - Pro B:294	[ RasMol ]
		Thr A:22 - Pro A:23	[ RasMol ]
		Thr B:22 - Pro B:23	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (6, 6)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (34, 34)

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