AMG-8718   Click here for help

GtoPdb Ligand ID: 9639

PDB Ligand
Compound class: Synthetic organic
Comment: This Amgen BACE1 inhibitor for Alzheimer's disease, AMG-8718, had a balanced profile of potency, hERG binding affinity, and Pgp recognition. It also produced robust and sustained reductions of CSF and brain Aβ levels in a rat pharmacodynamic model [1]. However, retinal thinning was observed in a 1-month toxicity study in the rat and further studies suggested this to be an off-target effect where, in the rat, AMG-8718 impairs phagolysosomal function, leading to photoreceptor dysfunction and ultimately loss of photoreceptors [2]. The compound is example 288 in [3] from over 1000 analogues, but only binned activity data is provided. While the PubChem Bioassay data and other sources link to this structure note that MMDB and PubMed link their PDB structure to a different tautomeric representation as PubChem CID 86580376.
Click here for help

Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

✖
Hydrogen bond acceptors 6
Hydrogen bond donors 1
Rotatable bonds 1
Topological polar surface area 91.85
Molecular weight 442.14
XLogP 3.48
No. Lipinski's rules broken 0
SMILES / InChI / InChIKey
Click here for help

SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

✖
Canonical SMILES NC1=NC2(CO1)c1cc(C#CC3(C)COC3)cnc1Oc1c2cc(cc1)c1cccnc1F
Isomeric SMILES NC1=N[C@]2(CO1)c1cc(C#CC3(C)COC3)cnc1Oc1c2cc(cc1)c1cccnc1F
InChI InChI=1S/C25H19FN4O3/c1-24(12-31-13-24)7-6-15-9-19-22(29-11-15)33-20-5-4-16(17-3-2-8-28-21(17)26)10-18(20)25(19)14-32-23(27)30-25/h2-5,8-11H,12-14H2,1H3,(H2,27,30)/t25-/m0/s1
InChI Key GKKFBOARESVMBW-VWLOTQADSA-N
Classification Click here for help
Compound class Synthetic organic
Database Links Click here for help
GtoPdb PubChem SID 340590269
PubChem CID 45254510
RCSB PDB Ligand 3LL
Search Google for chemical match using the InChIKey GKKFBOARESVMBW-VWLOTQADSA-N
Search Google for chemicals with the same backbone GKKFBOARESVMBW
SynPHARM 84541 (in complex with beta-secretase 1)
UniChem Compound Search for chemical match using the InChIKey GKKFBOARESVMBW-VWLOTQADSA-N
UniChem Connectivity Search for chemical match using the InChIKey GKKFBOARESVMBW-VWLOTQADSA-N