Structure of PDB 2fdp Chain C Binding Site BS01

Receptor Information
>2fdp Chain C (length=374) 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
VEDSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHV
HDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDFRP
InChIInChI=1S/C33H41FN4O3/c1-4-18-38(19-5-2)33(41)26-13-9-12-25(22-26)32(40)37-30(21-24-10-7-6-8-11-24)29(35)20-23(3)31(39)36-28-16-14-27(34)15-17-28/h6-17,22-23,29-30H,4-5,18-21,35H2,1-3H3,(H,36,39)(H,37,40)/t23-,29+,30+/m1/s1
InChIKeyPZHFCAIXAVDQAK-STQWGSIPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cccc(c1)C(=O)NC(Cc2ccccc2)C(CC(C)C(=O)Nc3ccc(cc3)F)N
CACTVS 3.341CCCN(CCC)C(=O)c1cccc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@@H](N)C[C@@H](C)C(=O)Nc3ccc(F)cc3
CACTVS 3.341CCCN(CCC)C(=O)c1cccc(c1)C(=O)N[CH](Cc2ccccc2)[CH](N)C[CH](C)C(=O)Nc3ccc(F)cc3
ACDLabs 10.04Fc3ccc(NC(=O)C(C)CC(N)C(NC(=O)c1cccc(C(=O)N(CCC)CCC)c1)Cc2ccccc2)cc3
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cccc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@H](C[C@@H](C)C(=O)Nc3ccc(cc3)F)N
FormulaC33 H41 F N4 O3
NameN1-((2S,3S,5R)-3-AMINO-6-(4-FLUOROPHENYLAMINO)-5-METHYL-6-OXO-1-PHENYLHEXAN-2-YL)-N3,N3-DIPROPYLISOPHTHALAMIDE
ChEMBLCHEMBL200077
DrugBank
ZINCZINC000010339558
PDB chain2fdp Chain C Residue 386 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2fdp Aminoethylenes: a tetrahedral intermediate isostere yielding potent inhibitors of the aspartyl protease BACE-1.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Q12 G13 D32 G34 S35 P70 Y71 T72 Q73 F108 I126 R128 D228 G230 T232
Binding residue
(residue number reindexed from 1)		Q15 G16 D35 G37 S38 P73 Y74 T75 Q76 F111 I129 R131 D220 G222 T224
Annotation score1
Binding affinityMOAD: Ki=0.026uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2fdp, PDBe:2fdp, PDBj:2fdp
PDBsum2fdp
PubMed16451048
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]