## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: IC50
- Label type: continuous
- Binary semantics: pchembl
- Assay description: KDR (VEGFR-2) Kinase Assay: The kinase used was a recombinant fusion protein composed of N-terminal GST and a C-terminal fragment of human KDR (amino acids D807-V1356), expressed in baculovirus-infected insect cells (Sf9) and purified by affinity chromatography (from ProQinase GmbH, Freiburg, Germany). The substrate used for the kinase reaction was the biotinylated peptide biotin-Ahx-DFGLARDMYDKEYYSVG (C terminus in acid form) (from Biosynthan GmbH, Berlin-Buch, Germany). For the assay, 50 nl of a 100-fold concentrated solution of the test substance in DMSO was pipetted into a black “low-volume 384 well” microtitre plate (from Greiner Bio-One, Frickenhausen, Germany), then 2 μl of a solution of KDR in assay buffer [50 mM HEPES/HCl pH 7, 25 mM MgCl2, 5 mM MnCl2, 1 mM dithiothreitol, 0.1 mM sodium orthovanadate, 0% (v/v) Nonidet-P40 (from Sigma)] was added and the mixture was incubated for 15 min, in order to enable preliminary binding of the substance to the enzyme before the kinase reaction. Then the kinase reaction was started by adding 3 μl of a solution of ATP (16.7 μM, final concentration in assay volume 5 μl is 10 μM) and substrate (0.83 μM, final concentration in assay volume 5 μl is 0.5 μM) in assay buffer and the resulting mixture was incubated at 22° C. for 45 min. The KDR concentration was adjusted with respect to the respective activity of the enzyme in such a way that the assay proceeded in the linear range. The reaction was stopped by adding 5 μl of a solution of HTRF detection reagents [0.1 μM streptavidin-XL665 (from Cisbio Bioassays, Codolet, France) and 2 nM PT66-Eu chelate, a europium chelate-labelled anti-phosphotyrosine antibody (from PerkinElmer), in aqueous EDTA solution (125 mM EDTA, 0.2% (w/v) BSA in 50 mM HEPES/HCl pH 7)]. The resulting mixture was incubated at 22° C. for 1 h to allow formation of a complex of the biotinylated phosphorylated substrate and the detection reagents. Subsequently, the amount of the phosphorylated substrate was evaluated by measuring the resonance energy transfer from the PT66-Eu chelate to the streptavidin-XL665. To this end, the fluorescence emissions at 620 nm and 665 nm after excitation at 350 nm were measured in an HTRF instrument [e.g. PHERAstar (from BMG Labtechnologies, Offenburg, Germany) or ViewLux (from PerkinElmer)]. The ratio of the emissions at 665 nm and 620 nm was taken as a measure of the amount of phosphorylated substrate. The data were normalized (enzyme reaction without inhibitor=0% inhibition; all other assay components except enzyme=100% inhibition). Typically, the test substances were tested on the same microtitre plate at 11 different concentrations in the range from 20 μM to 0.07 nM (20 μM, 5.7 μM, 1.6 μM, 0.47 μM, 0.13 μM, 38 nM, 11 nM, 3.1 nM, 0.89 nM, 0.25 nM and 0.07 nM) in twin values for each concentration. The dilution series were prepared by serial dilutions prior to the assay at the level of the 100-fold concentrated solution (i.e. 2 mM to 7.3 nM in 100% DMSO), although it was possible for the exact concentrations to be different depending on the pipettors used in each case. The IC50 values were calculated by a 4-parameter fit.
- Assay organism: Homo sapiens
- Target name: Vascular endothelial growth factor receptor 2
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: Cc1cc(F)c(Nc2ccnc3c2C(=O)Nc2cc(CN(C)C[C@@H](C)O)ccc2N3)cc1O
- Properties:
- ChEMBL ID: CHEMBL5941787
- Molecular weight: 451.5
- Heavy atoms: 33
- Hydrogen bond donors: 5
- Hydrogen bond acceptors: 7
- TPSA: 109.75
- LogP: 4.1
- Rotatable bonds: 6
- Ring count: 4
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.25
- QED: 0.38

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 9.14
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type IC50; relation =; value 0.73; units nM; pChEMBL 9.14; comment 486040

## Query Molecule B
- Canonical SMILES: Cc1cc(F)c(Nc2ccnc3c2C(=O)Nc2cc(CN(C)CCO)ccc2N3)cc1O
- Properties:
- ChEMBL ID: CHEMBL5780343
- Molecular weight: 437.48
- Heavy atoms: 32
- Hydrogen bond donors: 5
- Hydrogen bond acceptors: 7
- TPSA: 109.75
- LogP: 3.71
- Rotatable bonds: 6
- Ring count: 4
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.22
- QED: 0.4

## Molecule Similarity
- Weighted Tanimoto: 0.82

Answer: 9.07