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4DI2
Asym. Unit
Info
Asym.Unit (209 KB)
Biol.Unit 1 (72 KB)
Biol.Unit 2 (72 KB)
Biol.Unit 3 (71 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BACE1 IN COMPLEX WITH HYDROXYETHYLAMINE INHIBITOR 37
Authors
:
D. A. Whittington, A. M. Long
Date
:
30 Jan 12 (Deposition) - 10 Oct 12 (Release) - 19 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Memapsin-2, Alzheimer'S Disease, Protease, Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1, App, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. A. Dineen, M. M. Weiss, T. Williamson, P. Acton, S. Babu-Khan, M. D. Bartberger, J. Brown, K. Chen, Y. Cheng, M. Citron, M. D. Croghan, R. T. Dunn, J. Esmay, R. F. Graceffa, S. S. Harried, D. Hickman, S. A. Hitchcock, D. B. Horne, H. Huang, R. Imbeah-Ampiah, T. Judd, M. R. Kaller, C. R. Kreiman, D. S. La, V. Li, P. Lopez, S. Louie, H. Monenschein, T. T. Nguyen, L. D. Pennington, T. San Miguel, E. A. Sickmier, H. M. Vargas, R. C. Wahl, P. H. Wen, D. A. Whittington, S. Wood, Q. Xue, B. H. Yang, V. F. Patel, W. Zhong
Design And Synthesis Of Potent, Orally Efficacious Hydroxyethylamine Derived Beta-Site Amyloid Precursor Protein Cleaving Enzyme (Bace1) Inhibitors.
J. Med. Chem. V. 55 9025 2012
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: (2R)-N-{(2S,3R)-4-{[(4'S)-6'-(2,2-... (0K9a)
1b: (2R)-N-{(2S,3R)-4-{[(4'S)-6'-(2,2-... (0K9b)
1c: (2R)-N-{(2S,3R)-4-{[(4'S)-6'-(2,2-... (0K9c)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0K9
3
Ligand/Ion
(2R)-N-{(2S,3R)-4-{[(4'S)-6'-(2,2-DIMETHYLPROPYL)-3',4'-DIHYDROSPIRO[CYCLOBUTANE-1,2'-PYRANO[2,3-B]PYRIDIN]-4'-YL]AMINO}-3-HYDROXY-1-[3-(1,3-THIAZOL-2-YL)PHENYL]BUTAN-2-YL}-2-METHOXYPROPANAMIDE
2
GOL
5
Ligand/Ion
GLYCEROL
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:11 , GLN A:12 , GLY A:13 , LEU A:30 , ASP A:32 , GLY A:34 , SER A:35 , VAL A:69 , PRO A:70 , TYR A:71 , THR A:72 , ILE A:110 , ASP A:228 , GLY A:230 , THR A:231 , ARG A:235 , THR A:329 , HOH A:624 , HOH A:744 , HOH A:765 , HOH A:920
BINDING SITE FOR RESIDUE 0K9 A 501
2
AC2
SOFTWARE
ARG A:50 , TYR A:51
BINDING SITE FOR RESIDUE GOL A 502
3
AC3
SOFTWARE
LYS A:9 , SER A:10 , GLY A:11 , GLN A:12 , GLY A:13 , TYR A:14 , GLU A:339 , HOH A:687 , HOH A:832
BINDING SITE FOR RESIDUE GOL A 503
4
AC4
SOFTWARE
GLY B:11 , GLN B:12 , GLY B:13 , LEU B:30 , ASP B:32 , GLY B:34 , SER B:35 , PRO B:70 , TYR B:71 , THR B:72 , PHE B:108 , ILE B:110 , TYR B:198 , ASP B:228 , GLY B:230 , THR B:231 , ARG B:235 , THR B:329 , HOH B:639 , HOH B:659 , HOH B:798
BINDING SITE FOR RESIDUE 0K9 B 501
5
AC5
SOFTWARE
SER B:10 , GLY B:11 , GLN B:12 , GLY B:13 , TYR B:14 , GLU B:339 , HOH B:690
BINDING SITE FOR RESIDUE GOL B 502
6
AC6
SOFTWARE
THR B:292 , ASP B:378 , HOH B:719 , HOH B:766 , HOH B:824
BINDING SITE FOR RESIDUE GOL B 503
7
AC7
SOFTWARE
GLY C:11 , GLN C:12 , GLY C:13 , LEU C:30 , ASP C:32 , GLY C:34 , SER C:35 , VAL C:69 , PRO C:70 , TYR C:71 , THR C:72 , ASP C:228 , GLY C:230 , THR C:231 , THR C:329 , HOH C:650 , HOH C:797
BINDING SITE FOR RESIDUE 0K9 C 501
8
AC8
SOFTWARE
LYS C:9 , SER C:10 , GLY C:11 , GLN C:12 , GLY C:13 , TYR C:14 , VAL C:170 , GLU C:339 , HOH C:698 , HOH C:770
BINDING SITE FOR RESIDUE GOL C 502
[
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SAPs(SNPs)/Variants
(1, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_060692 (V204A, chain A/B/C, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_060692
V
265
A
BACE1_HUMAN
Polymorphism
28989503
A/B/C
V
204
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: PEPTIDASE_A1 (A:14-355,B:14-355,C:14-355)
2: ASP_PROTEASE (A:29-40,B:29-40,C:29-40)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEPTIDASE_A1
PS51767
Peptidase family A1 domain profile.
BACE1_HUMAN
75-416
3
A:14-355
B:14-355
C:14-355
2
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
BACE1_HUMAN
90-101
3
A:29-40
B:29-40
C:29-40
[
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Exons
(9, 27)
Info
All Exons
Exon 1.1b (A:-5-26 | B:-2-26 | C:-2-26)
Exon 1.2d (A:27-56 | B:27-56 | C:27-56)
Exon 1.4c (A:56-128 | B:56-128 | C:56-128)
Exon 1.5b (A:129-174 (gaps) | B:129-174 (gaps...)
Exon 1.6b (A:175-219 | B:175-219 | C:175-219)
Exon 1.7c (A:220-253 | B:220-253 | C:220-253)
Exon 1.8b (A:254-303 | B:254-303 | C:254-303)
Exon 1.9d (A:304-361 (gaps) | B:304-361 (gaps...)
Exon 1.10f (A:361-385 | B:361-385 | C:361-386)
View:
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All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2d
03: Boundary 1.2d/1.4c
04: Boundary 1.4c/1.5b
05: Boundary 1.5b/1.6b
06: Boundary 1.6b/1.7c
07: Boundary 1.7c/1.8b
08: Boundary 1.8b/1.9d
09: Boundary 1.9d/1.10f
10: Boundary 1.10f/-
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000313005
1b
ENSE00002169377
chr11:
117186972-117186251
722
BACE1_HUMAN
1-87
87
3
A:-5-26
B:-2-26
C:-2-26
32
29
29
1.2d
ENST00000313005
2d
ENSE00001779698
chr11:
117167677-117167589
89
BACE1_HUMAN
88-117
30
3
A:27-56
B:27-56
C:27-56
30
30
30
1.4c
ENST00000313005
4c
ENSE00001602221
chr11:
117166063-117165847
217
BACE1_HUMAN
117-189
73
3
A:56-128
B:56-128
C:56-128
73
73
73
1.5b
ENST00000313005
5b
ENSE00001732292
chr11:
117164724-117164587
138
BACE1_HUMAN
190-235
46
3
A:129-174 (gaps)
B:129-174 (gaps)
C:129-174 (gaps)
46
46
46
1.6b
ENST00000313005
6b
ENSE00001231658
chr11:
117163904-117163770
135
BACE1_HUMAN
236-280
45
3
A:175-219
B:175-219
C:175-219
45
45
45
1.7c
ENST00000313005
7c
ENSE00001053358
chr11:
117162529-117162428
102
BACE1_HUMAN
281-314
34
3
A:220-253
B:220-253
C:220-253
34
34
34
1.8b
ENST00000313005
8b
ENSE00001053366
chr11:
117161765-117161616
150
BACE1_HUMAN
315-364
50
3
A:254-303
B:254-303
C:254-303
50
50
50
1.9d
ENST00000313005
9d
ENSE00001385289
chr11:
117161375-117161204
172
BACE1_HUMAN
365-422
58
3
A:304-361 (gaps)
B:304-361 (gaps)
C:304-361 (gaps)
58
58
58
1.10f
ENST00000313005
10f
ENSE00002041784
chr11:
117160523-117156402
4122
BACE1_HUMAN
422-501
80
3
A:361-385
B:361-385
C:361-386
25
25
26
[
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SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d4di2a_ (A:)
1b: SCOP_d4di2b_ (B:)
1c: SCOP_d4di2c_ (C:)
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Protein Domains
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(
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Organisms
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)
(
)
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
d4di2a_
A:
1b
d4di2b_
B:
1c
d4di2c_
C:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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