4K9H - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   BACE-1 INHIBITOR COMPLEX

Authors :   S. R. Jordan

Date :   19 Apr 13 (Deposition) - 10 Jul 13 (Release) - 17 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.29

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

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

Reference :   L. D. Pennington, D. A. Whittington, M. D. Bartberger, S. R. Jordan, H. Monenschein, T. T. Nguyen, B. H. Yang, Q. M. Xue, F. Vounatsos, R. C. Wahl, K. Chen, S. Wood, M. Citron, V. F. Patel, S. A. Hitchcock, W. Zhong
Hydroxyethylamine-Based Inhibitors Of Bace1: P1-P3 Macrocyclization Can Improve Potency, Selectivity, And Cell Activity.
Bioorg. Med. Chem. Lett. V. 23 4459 2013
PubMed-ID: 23769639 | Reference-DOI: 10.1016/J.BMCL.2013.05.028

Molecule 1 - BETA-SECRETASE 1
	Chains	:	A, B, C
	EC Number	:	3.4.23.46
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 59-446
	Gene	:	BACE1, BACE, KIAA1149
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ASPARTYL PROTEASE 2, ASP2, ASP 2, BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA-SITE APP CLEAVING ENZYME 1, MEMAPSIN-2, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	1QU	3	Ligand/Ion	1-CYCLOPENTYL-N-[(2S,3R)-3-HYDROXY-1-PHENYL-4-{[3-(TRIFLUOROMETHYL)BENZYL]AMINO}BUTAN-2-YL]-6-OXO-5-(2-OXOPYRROLIDIN-1-YL)-1,6-DIHYDROPYRIDINE-3-CARBOXAMIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	1QU	1	Ligand/Ion	1-CYCLOPENTYL-N-[(2S,3R)-3-HYDROXY-1-PHENYL-4-{[3-(TRIFLUOROMETHYL)BENZYL]AMINO}BUTAN-2-YL]-6-OXO-5-(2-OXOPYRROLIDIN-1-YL)-1,6-DIHYDROPYRIDINE-3-CARBOXAMIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	1QU	1	Ligand/Ion	1-CYCLOPENTYL-N-[(2S,3R)-3-HYDROXY-1-PHENYL-4-{[3-(TRIFLUOROMETHYL)BENZYL]AMINO}BUTAN-2-YL]-6-OXO-5-(2-OXOPYRROLIDIN-1-YL)-1,6-DIHYDROPYRIDINE-3-CARBOXAMIDE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	1QU	1	Ligand/Ion	1-CYCLOPENTYL-N-[(2S,3R)-3-HYDROXY-1-PHENYL-4-{[3-(TRIFLUOROMETHYL)BENZYL]AMINO}BUTAN-2-YL]-6-OXO-5-(2-OXOPYRROLIDIN-1-YL)-1,6-DIHYDROPYRIDINE-3-CARBOXAMIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:32 , GLY A:34 , SER A:35 , PRO A:70 , TYR A:71 , THR A:72 , GLN A:73 , PHE A:108 , ASP A:228 , GLY A:230 , THR A:231 , THR A:232 , ASN A:233	BINDING SITE FOR RESIDUE 1QU A 401
2	AC2	SOFTWARE	ASP B:32 , GLY B:34 , SER B:35 , VAL B:69 , PRO B:70 , TYR B:71 , THR B:72 , GLN B:73 , ARG B:128 , ASP B:228 , GLY B:230 , THR B:231 , THR B:232 , ASN B:233	BINDING SITE FOR RESIDUE 1QU B 401
3	AC3	SOFTWARE	GLY C:11 , GLY C:13 , ASP C:32 , GLY C:34 , SER C:35 , PRO C:70 , TYR C:71 , THR C:72 , GLN C:73 , ILE C:110 , ASP C:228 , GLY C:230 , THR C:231 , THR C:232 , ASN C:233 , ARG C:235	BINDING SITE FOR RESIDUE 1QU C 401

Asymmetric Unit

No.	Residues
1	A:155	-	A:359
2	A:217	-	A:382
3	A:269	-	A:319
4	B:155	-	B:359
5	B:217	-	B:382
6	B:269	-	B:319
7	C:155	-	C:359
8	C:217	-	C:382
9	C:269	-	C:319

Asymmetric Unit

No.	Residues
1	Ser A:22	-	Pro A:23
2	Arg A:128	-	Pro A:129
3	Gly A:372	-	Pro A:373
4	Ser B:22	-	Pro B:23
5	Arg B:128	-	Pro B:129
6	Gly B:372	-	Pro B:373
7	Ser C:22	-	Pro C:23
8	Arg C:128	-	Pro C:129
9	Gly C:372	-	Pro C:373

(no "SAP(SNP)/Variant" information available for 4K9H)

(no "PROSITE Motif" information available for 4K9H)

(no "Exon" information available for 4K9H)

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:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4k9ha_ A: beta-secretase (memapsin)                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...eee.....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee........eeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeeee...eeeeeee...hhh.eeeeeeeee.......ee.eeeeee..ee...hhhhhhh..eee......eeeehhhhhhhhhhhhhhh.....hhhhhh....eee.....hhhhh..eeeeee.....eeeeeeehhhhheee..eeeee.eeee...eeehhhhhh.eeeeee....eeeeeee...........eeeeeee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9h A  -2 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 385
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157|      178       188       198       208       218       228       238       248       258       268       278       288       298       308||     325       335       345       355       365       375       385
                                                                                                                                                                                         157|                                                                                                                                         309|                                                                    
                                                                                                                                                                                          169                                                                                                                                          317

Chain B from PDB  Type:PROTEIN  Length:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4k9hb_ B: beta-secretase (memapsin)                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eee.....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee........eeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeee....eeeeee...hhh.eeeeeeeee..........eeeeee..ee.....hhhhh..eee......eeeehhhhhhhhhhhhhhh...............eee.....hhhhh..eeeeee.....eeeeeeehhhhheee..eeeee.eeee...eeehhhhhh.eeeeeehhh.eeeeeee...........eeeeeee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9h B  -2 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 385
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157|      179       189       199       209       219       229       239       249       259       269       279       289       299       309|      326       336       346       356       366       376         
                                                                                                                                                                                         157|                                                                                                                                        309|                                                                    
                                                                                                                                                                                          170                                                                                                                                         317

Chain C from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4k9hc_ C: beta-secretase (memapsin)                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...eee.....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee........eeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeee....eeeeeee...hhh.eeeeeeeee.......ee.eeeeee..ee...hhhhhh...eee......eeeehhhhhhhhhhhhhhh...............eee.....hhhhh..eeeee.......eeeeeehhhhheee..eeeee.eeee...eeehhhhhh.eeeeee....eeeeeee....ee..ee.eeeeee...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9h C  -2 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 385
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157|      178       188       198       208       218       228       238       248       258       268       278       288       298       308||     325       335       345       355       365       375       385
                                                                                                                                                                                         157|                                                                                                                                         309|                                                                    
                                                                                                                                                                                          169                                                                                                                                          317

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Pepsin-like (505)

Protein domain: beta-secretase (memapsin) (237)

Human (Homo sapiens) [TaxId: 9606] (237)

1a	d4k9ha_	A:
1b	d4k9hb_	B:
1c	d4k9hc_	C:

(no "CATH Domain" information available for 4K9H)

(no "Pfam Domain" information available for 4K9H)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Arg A:128 - Pro A:129	[ RasMol ]
		Arg B:128 - Pro B:129	[ RasMol ]
		Arg C:128 - Pro C:129	[ RasMol ]
		Gly A:372 - Pro A:373	[ RasMol ]
		Gly B:372 - Pro B:373	[ RasMol ]
		Gly C:372 - Pro C:373	[ RasMol ]
		Ser A:22 - Pro A:23	[ RasMol ]
		Ser B:22 - Pro B:23	[ RasMol ]
		Ser C:22 - Pro C:23	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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Access by PDB/NDB ID
	4k9h
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	3.4.23.46
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (9, 9)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (30, 30)

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