Structure of PDB 5qcu Chain A Binding Site BS01

Receptor Information

>5qcu Chain A (length=376) Species: 9606 (Homo sapiens)

SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGAVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEIN
GQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPD
GFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPV
EDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSAC
HVHDEFRTAAVEGPFVTLDMEDCGYN

Ligand information

• Ligand ID: E51
• InChI: InChI=1S/C26H42N2O5S/c1-5-6-12-27-25(30)19(3)14-24(29)23-13-18(2)10-11-21-8-7-9-22(15-21)17-34(32,33)16-20(4)26(31)28-23/h7-9,15,18-20,23-24,29H,5-6,10-14,16-17H2,1-4H3,(H,27,30)(H,28,31)/t18-,19-,20-,23+,24+/m1/s1
• InChIKey: RYVHNXNTYFQKLT-FSQPGOEKSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CCCCNC(=O)[C@H](C)C[C@@H]([C@@H]1C[C@@H](CCc2cccc(c2)CS(=O)(=O)C[C@H](C(=O)N1)C)C)O
  CACTVS 3.385: CCCCNC(=O)[C@H](C)C[C@H](O)[C@@H]1C[C@H](C)CCc2cccc(C[S](=O)(=O)C[C@@H](C)C(=O)N1)c2
  CACTVS 3.385: CCCCNC(=O)[CH](C)C[CH](O)[CH]1C[CH](C)CCc2cccc(C[S](=O)(=O)C[CH](C)C(=O)N1)c2
  ACDLabs 12.01: C1S(Cc2cc(CCC(CC(NC(C1C)=O)C(O)CC(C)C(NCCCC)=O)C)ccc2)(=O)=O
  OpenEye OEToolkits 2.0.6: CCCCNC(=O)C(C)CC(C1CC(CCc2cccc(c2)CS(=O)(=O)CC(C(=O)N1)C)C)O
• Formula: C26 H42 N2 O5 S
• Name: (2R,4S)-N-butyl-4-[(5S,8S,10R)-5,10-dimethyl-3,3,6-trioxo-3lambda~6~-thia-7-azabicyclo[11.3.1]heptadeca-1(17),13,15-trien-8-yl]-4-hydroxy-2-methylbutanamide
• PDB chain: 5qcu Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5qcu D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
• Resolution: 1.951 Å
• Binding residue (original residue number in PDB): G13 L30 D32 G34 Y71 T72 Q73 W115 D228 G230 T231 T232
• Binding residue (residue number reindexed from 1): G16 L33 D35 G37 Y74 T75 Q76 W118 D219 G221 T222 T223
• Annotation score: 1

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 D219 T222
• 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

External links

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