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4DH6
Biol. Unit 1
Info
Asym.Unit (69 KB)
Biol.Unit 1 (64 KB)
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(1)
Title
:
STRUCTURE OF BACE-1 (BETA-SECRETASE) IN COMPLEX WITH (2R)-N-((2S,3R)-1-(BENZO[D][1,3]DIOXOL-5-YL)-3-HYDROXY-4-((S)-6'-NEOPENTYL-3',4'-DIHYDROSPIRO[CYCLOBUTANE-1,2'-PYRANO[2,3-B]PYRIDINE]-4'-YLAMINO) BUTAN-2-YL)-2-METHOXYPROPANAMIDE
Authors
:
E. A. Sickmier
Date
:
27 Jan 12 (Deposition) - 18 Apr 12 (Release) - 03 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Bace-1, Beta-Secretase, Aspartyl Protease, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
M. M. Weiss, T. Williamson, S. Babu-Khan, M. D. Bartberger, J. Brown, K. Chen, Y. Cheng, M. Citron, M. D. Croghan, T. A. Dineen, 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, C. Rattan, T. San Miguel, E. A. Sickmier, R. C. Wahl, P. H. Wen, S. Wood, Q. Xue, B. H. Yang, V. F. Patel, W. Zhong
Design And Preparation Of A Potent Series Of Hydroxyethylamine Containing Beta-Secretase Inhibitors That Demonstrate Robust Reduction Of Central Beta-Amyloid.
J. Med. Chem. V. 55 9009 2012
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Hetero Components
(3, 11)
Info
All Hetero Components
1a: (2R)-N-[(2S,3R)-1-(1,3-BENZODIOXOL... (0KNa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: IODIDE ION (IODa)
3b: IODIDE ION (IODb)
3c: IODIDE ION (IODc)
3d: IODIDE ION (IODd)
3e: IODIDE ION (IODe)
3f: IODIDE ION (IODf)
3g: IODIDE ION (IODg)
3h: IODIDE ION (IODh)
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Label:
No.
Name
Count
Type
Full Name
1
0KN
1
Ligand/Ion
(2R)-N-[(2S,3R)-1-(1,3-BENZODIOXOL-5-YL)-4-{[(4'S)-6'-(2,2-DIMETHYLPROPYL)-3',4'-DIHYDROSPIRO[CYCLOBUTANE-1,2'-PYRANO[2,3-B]PYRIDIN]-4'-YL]AMINO}-3-HYDROXYBUTAN-2-YL]-2-METHOXYPROPANAMIDE
2
GOL
2
Ligand/Ion
GLYCEROL
3
IOD
8
Ligand/Ion
IODIDE ION
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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)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:104 , SER A:105
BINDING SITE FOR RESIDUE IOD A 401
2
AC2
SOFTWARE
TYR A:222
BINDING SITE FOR RESIDUE IOD A 405
3
AC3
SOFTWARE
TYR A:68
BINDING SITE FOR RESIDUE IOD A 406
4
AC4
SOFTWARE
TYR A:68 , PRO A:70 , LEU A:267
BINDING SITE FOR RESIDUE IOD A 407
5
AC5
SOFTWARE
GLN A:55 , LEU A:56 , ILE A:179 , HIS A:181 , TYR A:184 , LEU A:188
BINDING SITE FOR RESIDUE IOD A 408
6
AC6
SOFTWARE
LYS A:9 , GLY A:11 , GLN A:12 , GLY A:13 , SER A:229 , THR A:232 , ALA A:335 , GLU A:339 , HOH A:574
BINDING SITE FOR RESIDUE GOL A 409
7
AC7
SOFTWARE
ARG A:50 , TYR A:51 , HOH A:532
BINDING SITE FOR RESIDUE GOL A 410
8
AC8
SOFTWARE
LEU A:30 , ASP A:32 , GLY A:34 , SER A:35 , PRO A:70 , TYR A:71 , THR A:72 , PHE A:108 , ILE A:110 , TRP A:115 , ASP A:228 , GLY A:230 , THR A:231 , ARG A:235 , THR A:329
BINDING SITE FOR RESIDUE 0KN A 411
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_060692 (V204A, chain A, )
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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
V
204
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PEPTIDASE_A1 (A:14-355)
2: ASP_PROTEASE (A:29-40)
;
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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
1
A:14-355
2
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
BACE1_HUMAN
90-101
1
A:29-40
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d4dh6a_ (A:)
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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
d4dh6a_
A:
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CATH Domains
(0, 0)
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Pfam Domains
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Chain A
Asymmetric Unit 1
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Asym.Unit (69 KB)
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