Structure of PDB 6dmi Chain A Binding Site BS01

Receptor Information
>6dmi Chain A (length=374) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPH
PFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTV
RANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTH
VPNLFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRV
EINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVASIKAASSTEK
FPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYL
RPVSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHV
HDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID5T5
InChIInChI=1S/C19H16ClF2N3O3/c20-12-5-10(7-24-8-12)16(26)14-6-15(14)19(9-27-18(23)25-19)11-1-3-13(4-2-11)28-17(21)22/h1-5,7-8,14-15,17H,6,9H2,(H2,23,25)/t14-,15-,19-/m1/s1
InChIKeyAVRZQFKBYKMVDH-SPYBWZPUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=N[C@@](CO1)([C@@H]2C[C@H]2C(=O)c3cncc(Cl)c3)c4ccc(OC(F)F)cc4
CACTVS 3.385NC1=N[C](CO1)([CH]2C[CH]2C(=O)c3cncc(Cl)c3)c4ccc(OC(F)F)cc4
OpenEye OEToolkits 2.0.4c1cc(ccc1C2(COC(=N2)N)C3CC3C(=O)c4cc(cnc4)Cl)OC(F)F
OpenEye OEToolkits 2.0.4c1cc(ccc1[C@]2(COC(=N2)N)[C@@H]3C[C@H]3C(=O)c4cc(cnc4)Cl)OC(F)F
FormulaC19 H16 Cl F2 N3 O3
Name[(1~{R},2~{R})-2-[(4~{S})-2-azanyl-4-[4-[bis(fluoranyl)methoxy]phenyl]-5~{H}-1,3-oxazol-4-yl]cyclopropyl]-(5-chloranylpyridin-3-yl)methanone
ChEMBL
DrugBank
ZINCZINC000584905152
PDB chain6dmi Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6dmi qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G74 L91 D93 V130 Y132 I179 R189 D289 G291
Binding residue
(residue number reindexed from 1)		G18 L35 D37 V74 Y76 I123 R133 D222 G224
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D37 S40 N42 A44 Y76 D222 T225
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:6dmi, PDBe:6dmi, PDBj:6dmi
PDBsum6dmi
PubMed30457858
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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