4B78: Beta-secretase 1

Aminoimidazoles as BACE-1 Inhibitors: From De Novo Design to Ab- lowering in Brain. Determined by X-ray diffraction at 1.5 Å resolution. Released 26 Jun 2013.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 3,382
Mol. weight: 43.18 kDa
Ligands: KGG
Released: 26 Jun 2013

Explore 4B78 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4B78 contains 13 α-helices and 30 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
β-strand	14-20	7	1
β-strand	25-32	8	1
β-strand	38-41	4	1
α-helix	54-56	3
β-strand	61-70	10	1
β-strand	75-86	12	1
β-strand	94-106	13	1
β-strand	117-120	4	1
α-helix	124-126	3
α-helix	136-143	8
β-strand	150-155	6	1
β-strand	171-176	6	1
α-helix	181-183	3
β-strand	184-192	9	1
β-strand	196	1	2
β-strand	199	1	2
β-strand	200-201	2	3
β-strand	203-208	6	4
β-strand	211-212	2	4
α-helix	217-221	5
β-strand	225-227	3	3
β-strand	234-237	4	3
α-helix	238-251	14
α-helix	259-262	4
β-strand	268-270	3	5
α-helix	277-279	3
α-helix	281-282	2
β-strand	283-288	6	4
β-strand	294-300	7	4
α-helix	302-305	4
β-strand	306-308	3	5
α-helix	309	1
α-helix	312-314	3
β-strand	318-322	5	5
β-strand	324-327	4	3
β-strand	331-333	3	3
α-helix	335-338	4
β-strand	341-346	6	1
β-strand	351-357	7	1
β-strand	362	1	6
β-strand	367	1	6
β-strand	369-375	7	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-secretase 1	A	protein	384	HOMO SAPIENS	P56817 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4B78_1 BETA-SECRETASE 1 (chains A)
EMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTY
RDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILG
LAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGID
HSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKV
FEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITI
LPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACH
VHDEFRTAAVEGPFVTLDMEDCGY

Ligands and cofactors

ID	Name	Formula	Copies
KGG	(3R,5R)-3-methoxy-5-(4-methoxyphenyl)-5-(3-pyridin-3-ylphenyl)-3,4-dihydropyrro…	C23 H23 N3 O2	1

Primary citation

Core Refinement Toward Permeable Beta-Secretase (Bace-1) Inhibitors with Low Herg Activity. Ginman, T., Viklund, J., Malmstrom, J. et al. J Med Chem (2013) 56:4181. DOI 10.1021/JM3011349 · PubMed

Other PDB entries of the same protein (UniProt P56817 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MYI 1.25 Å, BACE-1 in complex with compound #6
6UWP 1.29 Å, BACE-1 in complex with compound #32
6EQM 1.35 Å, Crystal Structure of Human BACE-1 in Complex with CNP520
4L7G 1.38 Å, Diethylaminosulfur Trifluoride-Mediated Intramolecular Cyclization of…
6EJ2 1.46 Å, BACE1 compound 28
6UWV 1.47 Å, BACE-1 in complex with compound #34
3VF3 1.48 Å, Crystal Structure of Human Beta Secretase in Complex with NVP-BQQ711
5HDZ 1.49 Å, BACE-1 in complex with (7aR)-7a-(5-cyanothiophen-2-yl)-6-(5-fluoro-4-methyl-6-(methylthio…
2QP8 1.5 Å, Structure of BACE Bound to SCH734723
4DJX 1.5 Å, Structure of BACE Bound to 5-(3-(5-chloropyridin-3-yl)phenyl)-5-cyclopropyl-2-imino-3-met…
5HU1 1.5 Å, BACE1 in complex with (R)-N-(3-(3-amino-2,5-dimethyl-1,1-dioxido-5,6-dihydro-2H-1,2,4-thi…
6BFE 1.51 Å, BACE crystal structure with hydroxy pyrrolidine inhibitor

Browse structure collections

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