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ChEMBL-NTD

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ChEMBL-NTD Glossary

Compound Property Definitions

All properties are calculated on the parent form of the molecule i.e after any salts have been removed. Calculations are performed using algorithms available in pipeline pilot (accelrys).

Molecular Formula Molecular formula is written using the Hill System
Molecular Weight (MW) Molecular weight on the parent form of the molecule
ALogP Calculated value for the lipophilicity of a molecule expressed as log (octanol/water partition coefficient). Method used for the calculation is that defined by Ghose and Crippen.

Ghose, A.K., Viswanadhan V.N., and Wendoloski, J.J., Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragment Methods: An Analysis of AlogP and CLogP Methods. J. Phys. Chem. A, 1998, 102, 3762-3772.
Polar Surface Area (PSA) Polar surface area is calculated by the method by P Ertl.

Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties, Ertl, P., Rohde, B., Selzer, P., J. Med. Chem. 2000, 43, 3714-3717.
Hydrogen Bond Acceptors (HBA) Number Hydrogen Bond Acceptors. Where a hydrogen bond acceptor is defined as oxygen, nitrogen, sulphur, or phosphorus with one or more lone pairs. The following are excluded: atoms with positive formal charges, amide nitrogens, pyrrole-type nitrogens, aromatic oxygen and aromatic sulphur atoms.
Hydrogen Bond Donors (HBD) Number of Hydrogen Bond Donors. Where a hydrogen bond donor is defined as oxygen, nitrogen, sulphur, or phosphorus with one or more attached hydrogen atoms.
Rotatable Bonds (RTB) Number of rotatable bonds in the molecule. Rotatable bonds are defined as single bonds between heavy atoms. It doesn't include ring bonds, those connected to a heavy atom that is attached to only hydrogens or amide bonds.
Num Ro5 Violations (#Ro5 Vio.) Number of properties defined in Lipinski's Rule of 5 (RO5) that the compound fails. Conditions which violate the RO5 are:
Molecular weight>=500
AlogP >= 5
HBD >= 5
NplusOcount* >= 10

*NplusO count is the number of oxygen and nitrogen atoms in the molecule.

Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Adv. Drug Deliv. Rev., 1997, 23, 3-25.
Pass Rule of 3 It is suggested that compounds that pass all these criteria are more likely to be hits in fragment screening. Rule of 3 criteria:
molecular weight <= 300,
number of hydrogen bond donors <= 3,
number of hydrogen bond acceptors <= 3
AlogP <= 3
RTB <= 3
PSA <= 60

A 'Rule of Three' for fragment-based lead discovery? Miles Congreve, Robin Carr,Chris Murray and Harren Jhoti. Drug Discovery Today, 2003,8(19), 876-877
MedChem Friendly These are functional groups that may not be desirable from a medicinal chemistry perspective. For example reactive groups will be flagged as 'N' (not MedChem Friendly). Molecules which do not contain any of these groups will be flagged as 'Y' (MedChem Friendly). The groups are defined by the following list of SMARTS:
[N+]([O-])=O
[C;!R](-[C;!R]=O)=[C;!R]
C(-N)=S
P
O-N=C
OS(=O)=O
O1-CC-O-C-1
C(-N)=C
[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]
OC1OCC(O)C1
C=N-C(-O)
[N;H]-[C;H]-[N;H]
[C;!R]=[C;!R]-N-[C;D1&H3,D2&H2,D3&H1,D4]
[S;!R]-[C;!R]-[O;!R]
[O;D2]-[C;!H0](([F,Br,I,Cl])([F,Br,I,Cl])([!F,!Br,!I,!Cl]))
CC([O;!R])([O;!R])
C1-C-O1
C(=O)-S-C(=S)
[S;H]
SC#N
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