4DJX: BACE

Structure of BACE Bound to 5-(3-(5-chloropyridin-3-yl)phenyl)-5-cyclopropyl-2-imino-3-methylimidazolidin-4-one. Determined by X-ray diffraction at 1.5 Å resolution. Released 21 Mar 2012.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,115
Mol. weight: 93.48 kDa
Ligands: TLA, 0KQ
Released: 21 Mar 2012

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

Secondary structure: helices and β-sheets

4DJX 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	67-70	4	1
β-strand	74-81	8	1
β-strand	86-93	8	1
β-strand	99-102	4	1
α-helix	115-117	3
β-strand	122-132	11	1
β-strand	135-147	13	1
β-strand	155-167	13	1
β-strand	178-181	4	1
α-helix	185-187	3
α-helix	197-204	8
β-strand	211-215	5	1
α-helix	224-229	6
β-strand	233-237	5	1
α-helix	242-244	3
β-strand	245-253	9	1
β-strand	257	1	2
β-strand	260	1	2
β-strand	261	1	3
β-strand	264-269	6	4
β-strand	272-273	2	4
α-helix	278-282	5
β-strand	286-288	3	3
β-strand	295-298	4	3
α-helix	299-312	14
α-helix	320-323	4
β-strand	329-331	3	5
α-helix	338-340	3
α-helix	342-343	2
β-strand	344-349	6	4
β-strand	355-361	7	4
α-helix	363-366	4
β-strand	367-370	4	5
β-strand	379-383	5	5
β-strand	385-388	4	3
β-strand	392-394	3	3
α-helix	396-399	4
β-strand	402-407	6	1
β-strand	412-418	7	1
β-strand	430-436	7	4
α-helix	440-443	4

Chain B: 13 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	67-70	4	6
β-strand	74-81	8	6
β-strand	86-93	8	6
β-strand	99-102	4	6
α-helix	115-117	3
β-strand	122-132	11	6
β-strand	135-147	13	6
β-strand	155-167	13	6
β-strand	178-181	4	6
α-helix	185-187	3
α-helix	197-204	8
β-strand	211-215	5	6
α-helix	224-229	6
β-strand	233-237	5	6
α-helix	242-244	3
β-strand	245-253	9	6
β-strand	257	1	7
β-strand	260	1	7
β-strand	261-262	2	8
β-strand	264-269	6	9
β-strand	272-273	2	9
α-helix	278-282	5
β-strand	286-288	3	8
β-strand	295-298	4	8
α-helix	299-312	14
α-helix	320-323	4
β-strand	329-331	3	10
α-helix	338-340	3
α-helix	342-343	2
β-strand	344-349	6	9
β-strand	355-361	7	9
α-helix	363-366	4
β-strand	367-370	4	10
β-strand	379-383	5	10
β-strand	385-388	4	8
β-strand	392-394	3	8
α-helix	396-399	4
β-strand	402-407	6	6
β-strand	412-418	7	6
β-strand	430-436	7	9
α-helix	440-443	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-secretase 1	A, B	protein	414	Homo sapiens	P56817 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4DJX_1 Beta-secretase 1 (chains A, B)
LRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFA
VGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANI
AAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGF
PLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKE
YNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNI
FPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIME
GFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST

Ligands and cofactors

ID	Name	Formula	Copies
TLA	L(+)-tartaric acid	C4 H6 O6	2
0KQ	(2E,5R)-5-[3-(5-chloropyridin-3-yl)phenyl]-5-cyclopropyl-2-imino-3-methylimidaz…	C18 H17 Cl N4 O	2

Primary citation

Structure based design of iminohydantoin BACE1 inhibitors: Identification of an orally available, centrally active BACE1 inhibitor. Cumming, J.N., Smith, E.M., Wang, L. et al. Bioorg Med Chem Lett (2012) 22:2444-2449. DOI 10.1016/j.bmcl.2012.02.013 · 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
4B78 1.5 Å, Aminoimidazoles as BACE-1 Inhibitors: From De Novo Design to Ab- lowering in Brain
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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