Structure of PDB 6nv7 Chain B Binding Site BS01

Receptor Information

>6nv7 Chain B (length=370) Species: 9606 (Homo sapiens)

GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGSVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFR
TAAVEGPFVTLDMEDCGYNI

Ligand information

• Ligand ID: L3J
• InChI: InChI=1S/C32H46N4O5S/c1-6-14-36(42(5,40)41)29-18-26-11-8-7-10-24-12-9-13-25(15-24)17-28(35-31(38)27(16-26)19-29)21-33-30(23(4)37)32(39)34-20-22(2)3/h9,12-13,15-16,18-20,22-23,28,30,33,37H,6-8,10-11,14,17,21H2,1-5H3,(H,35,38)/b34-20+/t23-,28-,30+/m0/s1
• InChIKey: DQMUZJCEBNKYBU-PQJSMVLXSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCCN(c1cc2cc(c1)C(=O)N[C@@H](Cc3cccc(c3)CCCC2)CN[C@H]([C@H](C)O)C(=O)/N=C/C(C)C)S(=O)(=O)C
  ACDLabs 12.01: C(\C=N\C(C(NCC2NC(=O)c1cc(cc(N(CCC)S(C)(=O)=O)c1)CCCCc3cccc(C2)c3)C(C)O)=O)(C)C
  CACTVS 3.385: CCCN(c1cc2CCCCc3cccc(C[C@@H](CN[C@H]([C@H](C)O)C(=O)N=CC(C)C)NC(=O)c(c2)c1)c3)[S](C)(=O)=O
  OpenEye OEToolkits 2.0.7: CCCN(c1cc2cc(c1)C(=O)NC(Cc3cccc(c3)CCCC2)CNC(C(C)O)C(=O)N=CC(C)C)S(=O)(=O)C
  CACTVS 3.385: CCCN(c1cc2CCCCc3cccc(C[CH](CN[CH]([CH](C)O)C(=O)N=CC(C)C)NC(=O)c(c2)c1)c3)[S](C)(=O)=O
• Formula: C32 H46 N4 O5 S
• Name: (E)-N-(2-methylpropylidene)-N~2~-{[(4S)-17-[(methylsulfonyl)(propyl)amino]-2-oxo-3-azatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaen-4-yl]methyl}-D-threoninamide
• PDB chain: 6nv7 Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6nv7 Development of an Efficient Enzyme Production and Structure-Based Discovery Platform for BACE1 Inhibitors.
• Resolution: 2.132 Å
• Binding residue (original residue number in PDB): G11 L30 D32 G34 P70 Y71 T72 Q73 F108 Y198 D228 G230 T231 T232 N233 R235
• Binding residue (residue number reindexed from 1): G15 L34 D36 G38 P74 Y75 T76 Q77 F112 Y190 D220 G222 T223 T224 N225 R227
• Annotation score: 1
• Binding affinity: MOAD: Ki=5nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D32 S35 N37 A39 Y71 D228 T231
• Catalytic site (residue number reindexed from 1): D36 S39 N41 A43 Y75 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

External links

• PDB: RCSB:6nv7, PDBe:6nv7, PDBj:6nv7
• PDBsum: 6nv7
• PubMed: 31549827
• UniProt: P56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)