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Receptor Information

>5qdb 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 ID

BAV

InChI

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

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	CC1CCCCCCCCC(=O)N(C(C(=O)NC(C1)C(CNCc2cccc(c2)C(C)C)O)C)C
OpenEye OEToolkits 1.5.0	C[C@@H]1CCCCCCCCC(=O)N([C@H](C(=O)N[C@@H](C1)[C@@H](CNCc2cccc(c2)C(C)C)O)C)C
CACTVS 3.341	CC(C)c1cccc(CNC[C@@H](O)[C@@H]2C[C@H](C)CCCCCCCCC(=O)N(C)[C@@H](C)C(=O)N2)c1
CACTVS 3.341	CC(C)c1cccc(CNC[CH](O)[CH]2C[CH](C)CCCCCCCCC(=O)N(C)[CH](C)C(=O)N2)c1
ACDLabs 10.04	O=C2NC(C(O)CNCc1cccc(c1)C(C)C)CC(C)CCCCCCCCC(=O)N(C)C2C

Formula

C29 H49 N3 O3

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;
(3S,14R,16S)-16-[(R)-1-Hydroxy-2-(3-isopropyl-benzylamino)-ethyl]-3,4,14-trimethyl-1,4diaza-cyclohexadecane-2,5-dione

PDB chain

5qdb 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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Structure summary

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PDB	5qdb D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Resolution	2.1 Å
Binding residue (original residue number in PDB)	Q12 L30 D32 G34 Y71 T72 Q73 W115 D228 G230 T231 T232
Binding residue (residue number reindexed from 1)	Q15 L33 D35 G37 Y74 T75 Q76 W118 D220 G222 T223 T224
Annotation score	1

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.

	Molecular Function
GO:0004190	aspartic-type endopeptidase activity

	Biological Process
GO:0006508	proteolysis

	Cellular Component
GO:0016020	membrane

PDB	RCSB:5qdb, PDBe:5qdb, PDBj:5qdb
PDBsum	5qdb
PubMed	31974851
UniProt	P56817\|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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Structure of PDB 5qdb Chain A Binding Site BS01