Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T79031 Target Info
Target Name Beta-secretase 1 (BACE1)
Synonyms Membrane-associated aspartic protease 2; Memapsin-2; KIAA1149; Beta-site amyloid precursor protein cleaving enzyme 1; Beta-site APP cleaving enzyme 1; BACE; Aspartyl protease 2; Asp 2; ASP2
Target Type Clinical trial Target
Gene Name BACE1
Biochemical Class Peptidase
UniProt ID
BACE1_HUMAN
Ligand General Information  Top
Ligand Name (3S,14R,16S)-16-[(1R)-1-hydroxy-2-{[3-(1-methylethyl)benzyl]amino}ethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5-dione Ligand Info
Canonical SMILES CC1CCCCCCCCC(=O)N(C(C(=O)NC(C1)C(CNCC2=CC(=CC=C2)C(C)C)O)C)C
InChI 1S/C29H49N3O3/c1-21(2)25-15-12-14-24(18-25)19-30-20-27(33)26-17-22(3)13-10-8-6-7-9-11-16-28(34)32(5)23(4)29(35)31-26/h12,14-15,18,21-23,26-27,30,33H,6-11,13,16-17,19-20H2,1-5H3,(H,31,35)/t22-,23+,26+,27-/m1/s1
InChIKey LHBBUGLYVFZUTH-GXVHRJHYSA-N
PubChem Compound ID 25163982
Drug Binding Sites of Target  Top
PDB ID: 3DV5      Crystal structure of human beta-secretase in complex with NVP-BAV544
Method X-ray diffraction Resolution 2.10 Å Mutation No [1]
PDB Sequence
SFVEMVDNLR
7
GKSGQGYYVE
17
MTVGSPPQTL
27
NILVDTGSSN
37
FAVGAAPHPF
47

LHRYYQRQLS
57
STYRDLRKGV
67
YVPYTQGKWE
77
GELGTDLVSI
87
PHGPNVTVRA
97

NIAAITESDK
107
FFINGSNWEG
117
ILGLAYAEIA
127
RPDDSLEPFF
137
DSLVKQTHVP
147

NLFSLQLCGA
157
SVGGSMIIGG
178
IDHSLYTGSL
188
WYTPIRREWY
198
YEVIIVRVEI
208

NGQDLKMDCK
218
EYNYDKSIVD
228
SGTTNLRLPK
238
KVFEAAVKSI
248
KAASSTEKFP
258

DGFWLGEQLV
268
CWQAGTTPWN
278
IFPVISLYLM
288
GEVTNQSFRI
298
TILPQQYLRP
308

VEDVATSQDD
318
CYKFAISQSS
328
TGTVMGAVIM
338
EGFYVVFDRA
348
RKRIGFAVSA
358

CHVHDEFRTA
368
AVEGPFVTLD
378
MEDCGYN
Residue
Distance (Å)
GLY11
3.752
GLN12
3.533
GLY13
3.740
LEU30
3.780
ASP32
2.631
GLY34
3.188
SER35
3.605
VAL69
3.516
PRO70
3.501
TYR71
3.294
THR72
3.059
GLN73
3.357
PHE108
3.855
Residue
Distance (Å)
ILE110
3.984
TRP115
3.658
ILE118
3.887
ILE126
3.871
TYR198
3.738
ILE226
4.079
ASP228
2.651
GLY230
3.025
THR231
3.276
THR232
2.850
ASN233
4.637
ARG235
4.433
PDB ID: 5QDB      Crystal structure of BACE complex with BMC002
Method X-ray diffraction Resolution 2.10 Å Mutation No [2]
PDB Sequence
SFVEMVDNLR
7
GKSGQGYYVE
17
MTVGSPPQTL
27
NILVDTGSSN
37
FAVGAAPHPF
47

LHRYYQRQLS
57
STYRDLRKGV
67
YVPYTQGKWE
77
GELGTDLVSI
87
PHGPNVTVRA
97

NIAAITESDK
107
FFINGSNWEG
117
ILGLAYAEIA
127
RPDDSLEPFF
137
DSLVKQTHVP
147

NLFSLQLCGA
157
SVGGSMIIGG
178
IDHSLYTGSL
188
WYTPIRREWY
198
YEVIIVRVEI
208

NGQDLKMDCK
218
EYNYDKSIVD
228
SGTTNLRLPK
238
KVFEAAVKSI
248
KAASSTEKFP
258

DGFWLGEQLV
268
CWQAGTTPWN
278
IFPVISLYLM
288
GEVTNQSFRI
298
TILPQQYLRP
308

VEDVATSQDD
318
CYKFAISQSS
328
TGTVMGAVIM
338
EGFYVVFDRA
348
RKRIGFAVSA
358

CHVHDEFRTA
368
AVEGPFVTLD
378
MEDCGYN
Residue
Distance (Å)
GLY11
3.652
GLN12
3.542
GLY13
3.792
LEU30
3.664
ASP32
2.601
GLY34
3.180
SER35
3.698
VAL69
3.477
PRO70
3.520
TYR71
3.344
THR72
3.068
GLN73
3.316
PHE108
3.835
Residue
Distance (Å)
ILE110
3.945
TRP115
3.626
ILE118
3.812
ILE126
3.818
TYR198
3.730
ILE226
4.079
ASP228
2.650
GLY230
3.014
THR231
3.253
THR232
2.856
ASN233
4.634
ARG235
4.498
References  Top
REF 1 Macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors with activity in vivo. Bioorg Med Chem Lett. 2009 Mar 1;19(5):1366-70.
REF 2 D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des. 2020 Feb;34(2):99-119.

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