7MYI: BACE-1

BACE-1 in complex with compound #6. Determined by X-ray diffraction at 1.25 Å resolution. Released 21 Jul 2021.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,604
Mol. weight: 98.76 kDa
Ligands: ZQS
Released: 21 Jul 2021

Explore 7MYI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7MYI contains 26 α-helices and 56 β-strands across 2 chains. 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, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
β-strand	13-20	8	1
β-strand	25-32	8	1
β-strand	38-41	4	1
α-helix	54-56	3
β-strand	61-71	11	1
β-strand	74-86	13	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	150-154	5	1
α-helix	163-168	6
β-strand	172-176	5	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	306-309	4	5
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	369-375	7	4
α-helix	379-382	4

Chain B: 13 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	6
β-strand	13-20	8	6
β-strand	25-32	8	6
β-strand	38-41	4	6
α-helix	54-56	3
β-strand	61-71	11	6
β-strand	74-86	13	6
β-strand	94-106	13	6
β-strand	117-120	4	6
α-helix	124-126	3
α-helix	136-143	8
β-strand	150-154	5	6
α-helix	163-168	6
β-strand	172-176	5	6
α-helix	181-183	3
β-strand	184-192	9	6
β-strand	196	1	7
β-strand	199	1	7
β-strand	200	1	8
β-strand	203-208	6	9
β-strand	211-212	2	9
α-helix	217-221	5
β-strand	225-227	3	8
β-strand	234-237	4	8
α-helix	238-251	14
α-helix	259-262	4
β-strand	268-270	3	10
α-helix	277-279	3
α-helix	281-282	2
β-strand	283-288	6	9
β-strand	294-300	7	9
α-helix	302-305	4
β-strand	306-309	4	10
β-strand	318-322	5	10
β-strand	324-327	4	8
β-strand	331-333	3	8
α-helix	335-338	4
β-strand	341-346	6	6
β-strand	351-357	7	6
β-strand	369-375	7	9
α-helix	379-382	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-secretase 1	A, B	protein	442	Homo sapiens	P56817 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7MYI_1 Beta-secretase 1 (chains A, B)
MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSG
QGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPY
TQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDD
SLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYT
PIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAA
SSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVED
VATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVE
GPFVTLDMEDCGYNIPQTDEST

Ligands and cofactors

ID	Name	Formula	Copies
ZQS	(4aR,7aR)-6-(pyrimidin-2-yl)-7a-(thiophen-2-yl)-4,4a,5,6,7,7a-hexahydropyrrolo[…	C14 H15 N5 S2	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Discovery and Early Clinical Development of LY3202626, a Low-Dose, CNS-Penetrant BACE Inhibitor. McKinzie, D.L., Winneroski, L.L., Green, S.J. et al. J Med Chem (2021) 64:8076-8100. DOI 10.1021/acs.jmedchem.1c00489 · PubMed

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

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
4B78 1.5 Å, Aminoimidazoles as BACE-1 Inhibitors: From De Novo Design to Ab- lowering in Brain
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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