Structure of PDB 3r2f Chain A Binding Site BS01

Receptor Information
>3r2f Chain A (length=386) 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
RKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGY
Ligand information
Ligand IDPB0
InChIInChI=1S/C36H50F2N4O5/c1-5-15-47-29-20-30(39-22-29)33(44)31(18-26-16-27(37)19-28(38)17-26)40-34(45)32(12-11-25-9-7-6-8-10-25)42-14-13-36(35(42)46,21-23(2)3)41-24(4)43/h6-10,16-17,19,23,29-33,39,44H,5,11-15,18,20-22H2,1-4H3,(H,40,45)(H,41,43)/t29-,30-,31+,32+,33-,36+/m1/s1
InChIKeyLPZOLMFQGUDKQH-ZXWXCOCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCO[C@@H]1C[C@@H](NC1)[C@H]([C@H](Cc2cc(cc(c2)F)F)NC(=O)[C@H](CCc3ccccc3)N4CC[C@@](C4=O)(CC(C)C)NC(=O)C)O
ACDLabs 12.01Fc1cc(cc(F)c1)CC(NC(=O)C(N2C(=O)C(NC(=O)C)(CC2)CC(C)C)CCc3ccccc3)C(O)C4NCC(OCCC)C4
CACTVS 3.370CCCO[C@H]1CN[C@H](C1)[C@@H](O)[C@H](Cc2cc(F)cc(F)c2)NC(=O)[C@H](CCc3ccccc3)N4CC[C@@](CC(C)C)(NC(C)=O)C4=O
OpenEye OEToolkits 1.7.0CCCOC1CC(NC1)C(C(Cc2cc(cc(c2)F)F)NC(=O)C(CCc3ccccc3)N4CCC(C4=O)(CC(C)C)NC(=O)C)O
CACTVS 3.370CCCO[CH]1CN[CH](C1)[CH](O)[CH](Cc2cc(F)cc(F)c2)NC(=O)[CH](CCc3ccccc3)N4CC[C](CC(C)C)(NC(C)=O)C4=O
FormulaC36 H50 F2 N4 O5
Name(2S)-2-[(3R)-3-(acetylamino)-3-(2-methylpropyl)-2-oxopyrrolidin-1-yl]-N-{(1R,2S)-3-(3,5-difluorophenyl)-1-hydroxy-1-[(2R,4R)-4-propoxypyrrolidin-2-yl]propan-2-yl}-4-phenylbutanamide
ChEMBLCHEMBL1915990
DrugBank
ZINCZINC000082140785
PDB chain3r2f Chain A Residue 394 [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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PDB3r2f Monosubstituted {gamma}-lactam and conformationally constrained 1,3-diaminopropan-2-ol transition-state isostere inhibitors of {beta}-secretase (BACE).
Resolution2.53 Å
Binding residue
(original residue number in PDB)		D32 G34 Y71 T72 Q73 F108 I110 W115 Y198 D228 G230 T231 T232 R235
Binding residue
(residue number reindexed from 1)		D34 G36 Y73 T74 Q75 F110 I112 W117 Y200 D230 G232 T233 T234 R237
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.85,IC50=1.4nM
BindingDB: IC50=1.4nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
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:3r2f, PDBe:3r2f, PDBj:3r2f
PDBsum3r2f
PubMed21782431
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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