Structure of PDB 5qd7 Chain A Binding Site BS01

Receptor Information
>5qd7 Chain A (length=377) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSA
CHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID0BI
InChIInChI=1S/C35H45N3O4/c1-24(2)27-9-7-10-29(20-27)35(12-13-35)37-22-33(39)32-19-25-8-6-11-31(18-25)42-15-5-4-14-36-30-17-26(23-41-3)16-28(21-30)34(40)38-32/h6-11,16-18,20-21,24,32-33,36-37,39H,4-5,12-15,19,22-23H2,1-3H3,(H,38,40)/t32-,33+/m0/s1
InChIKeyGCZHKZTYTMTFGU-JHOUSYSJSA-N
SMILES
SoftwareSMILES
CACTVS 3.352COCc1cc2NCCCCOc3cccc(C[C@H](NC(=O)c(c1)c2)[C@H](O)CNC4(CC4)c5cccc(c5)C(C)C)c3
OpenEye OEToolkits 1.7.0CC(C)c1cccc(c1)C2(CC2)NCC(C3Cc4cccc(c4)OCCCCNc5cc(cc(c5)C(=O)N3)COC)O
OpenEye OEToolkits 1.7.0CC(C)c1cccc(c1)C2(CC2)NC[C@H]([C@@H]3Cc4cccc(c4)OCCCCNc5cc(cc(c5)C(=O)N3)COC)O
CACTVS 3.352COCc1cc2NCCCCOc3cccc(C[CH](NC(=O)c(c1)c2)[CH](O)CNC4(CC4)c5cccc(c5)C(C)C)c3
FormulaC35 H45 N3 O4
Name(4S)-4-[(1R)-1-hydroxy-2-({1-[3-(1-methylethyl)phenyl]cyclopropyl}amino)ethyl]-19-(methoxymethyl)-11-oxa-3,16-diazatric yclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one;
(S)-4-{(R)-1-Hydroxy-2-[1-(3-isopropyl-phenyl)-cyclopropylamino]-ethyl}-19-methoxymethyl-11-oxa 3,16-diaza-tricyclo[15.3.1.1*6,10*]docosa-1(21),6,8,10(22),17 ,19-hexaen-2-one
ChEMBLCHEMBL595066
DrugBank
ZINCZINC000043203209
PDB chain5qd7 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5qd7 D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		G11 Q12 L30 D32 G34 Y71 T72 Q73 F108 I110 W115 Y198 I226 D228 G230 T231 T232 R235
Binding residue
(residue number reindexed from 1)		G14 Q15 L33 D35 G37 Y74 T75 Q76 F111 I113 W118 Y190 I218 D220 G222 T223 T224 R227
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 D220 T223
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:5qd7, PDBe:5qd7, PDBj:5qd7
PDBsum5qd7
PubMed31974851
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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