Structure of PDB 3k5d Chain A Binding Site BS01

Receptor Information
>3k5d Chain A (length=375) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGAGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEING
QDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDG
FWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVE
DVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACH
VHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDXLI
InChIInChI=1S/C27H52N4O5S/c1-9-10-12-28-25(34)19(6)16-24(33)22(14-17(2)3)31-26(35)21(11-13-37-8)30-27(36)23(15-18(4)5)29-20(7)32/h17-19,21-24,33H,9-16H2,1-8H3,(H,28,34)(H,29,32)(H,30,36)(H,31,35)/t19-,21+,22+,23+,24+/m1/s1
InChIKeyPEWRQHFGBBTOMS-FFYZIMEISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCCNC(=O)C(C)CC(C(CC(C)C)NC(=O)C(CCSC)NC(=O)C(CC(C)C)NC(=O)C)O
ACDLabs 12.01O=C(NC(C(=O)NC(CC(C)C)C(O)CC(C(=O)NCCCC)C)CCSC)C(NC(=O)C)CC(C)C
OpenEye OEToolkits 1.7.0CCCCNC(=O)[C@H](C)C[C@@H]([C@H](CC(C)C)NC(=O)[C@H](CCSC)NC(=O)[C@H](CC(C)C)NC(=O)C)O
CACTVS 3.370CCCCNC(=O)[C@H](C)C[C@H](O)[C@H](CC(C)C)NC(=O)[C@H](CCSC)NC(=O)[C@H](CC(C)C)NC(C)=O
CACTVS 3.370CCCCNC(=O)[CH](C)C[CH](O)[CH](CC(C)C)NC(=O)[CH](CCSC)NC(=O)[CH](CC(C)C)NC(C)=O
FormulaC27 H52 N4 O5 S
NameN-acetyl-L-leucyl-N-[(4S,5S,7R)-8-(butylamino)-5-hydroxy-2,7-dimethyl-8-oxooctan-4-yl]-L-methioninamide
ChEMBLCHEMBL1097361
DrugBank
ZINCZINC000044460279
PDB chain3k5d Chain A Residue 393 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3k5d Structure-based design and synthesis of novel P2/P3 modified, non-peptidic beta-secretase (BACE-1) inhibitors.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		G11 Q12 D32 G34 Y71 T72 Q73 F108 D228 G230 T231 T232
Binding residue
(residue number reindexed from 1)		G14 Q15 D35 G37 Y74 T75 Q76 F111 D218 G220 T221 T222
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.28,IC50=53nM
BindingDB: IC50=53nM
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 D218 T221
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3k5d, PDBe:3k5d, PDBj:3k5d
PDBsum3k5d
PubMed20172717
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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