Structure of PDB 4gid Chain A Binding Site BS01

Receptor Information
>4gid Chain A (length=387) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWY
YEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSI
KAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRI
TILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRA
RKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID0GH
InChIInChI=1S/C35H47N5O6S/c1-23(2)21-37-35(44)32(25(4)41)36-22-30(17-26-13-9-7-10-14-26)39-34(43)29-18-28(19-31(20-29)40(5)47(6,45)46)33(42)38-24(3)27-15-11-8-12-16-27/h7-16,18-20,23-25,30,32,36,41H,17,21-22H2,1-6H3,(H,37,44)(H,38,42)(H,39,43)/t24-,25-,30+,32+/m1/s1
InChIKeyUZFAOTIMARRSKT-TYUOOWEOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C[C@H](c1ccccc1)NC(=O)c2cc(cc(c2)N(C)S(=O)(=O)C)C(=O)N[C@@H](Cc3ccccc3)CN[C@@H]([C@@H](C)O)C(=O)NCC(C)C
CACTVS 3.370CC(C)CNC(=O)[C@@H](NC[C@H](Cc1ccccc1)NC(=O)c2cc(cc(c2)C(=O)N[C@H](C)c3ccccc3)N(C)[S](C)(=O)=O)[C@@H](C)O
CACTVS 3.370CC(C)CNC(=O)[CH](NC[CH](Cc1ccccc1)NC(=O)c2cc(cc(c2)C(=O)N[CH](C)c3ccccc3)N(C)[S](C)(=O)=O)[CH](C)O
OpenEye OEToolkits 1.7.6CC(C)CNC(=O)C(C(C)O)NCC(Cc1ccccc1)NC(=O)c2cc(cc(c2)N(C)S(=O)(=O)C)C(=O)NC(C)c3ccccc3
ACDLabs 12.01O=S(=O)(N(c1cc(cc(c1)C(=O)NC(Cc2ccccc2)CNC(C(=O)NCC(C)C)C(O)C)C(=O)NC(c3ccccc3)C)C)C
FormulaC35 H47 N5 O6 S
NameN-[(2S)-1-({(2S,3R)-3-hydroxy-1-[(2-methylpropyl)amino]-1-oxobutan-2-yl}amino)-3-phenylpropan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide
ChEMBLCHEMBL2179132
DrugBank
ZINCZINC000068208822
PDB chain4gid Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4gid Structure-based design of highly selective beta-secretase inhibitors: synthesis, biological evaluation, and protein-ligand X-ray crystal structure.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G59 Q60 G61 L78 D80 G82 Y119 T120 Q121 F156 D276 G278 T279 T280 N281 R283
Binding residue
(residue number reindexed from 1)		G13 Q14 G15 L32 D34 G36 Y73 T74 Q75 F110 D230 G232 T233 T234 N235 R237
Annotation score1
Binding affinityMOAD: Ki=0.017nM
PDBbind-CN: -logKd/Ki=10.77,Ki=0.017nM
Enzymatic activity
Catalytic site (original residue number in PDB) D80 S83 N85 A87 Y119 D276 T279
Catalytic site (residue number reindexed from 1) D34 S37 N39 A41 Y73 D230 T233
Enzyme Commision number 3.4.23.46: memapsin 2.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4gid, PDBe:4gid, PDBj:4gid
PDBsum4gid
PubMed22954357
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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