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Table 2 Average values of descriptors characterizing polar molecular surface area, H-bond donors, H-bond acceptors, partition coefficient and rotatable bonds for ordinary molecules, ligands and ligands with different protein-binding potentials

From: Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery

Descriptor*

Small molecules†

Average values

Standard error

Number of molecules

PSA

Molecules

111.81

1.79

2,184

 

Ligands

230.59

2.79

2,176

 

Ligands (≤ 3)

225.71

2.80

2,072

 

Ligands (4-9)

304.28

15.67

80

 

Ligands (≥ 10)

406.83

33.10

24

Donor

Molecules

1.51

0.04

2,184

 

Ligands

3.97

0.07

2,176

 

Ligands (≤ 3)

3.87

0.07

2,072

 

Ligands (4-9)

5.24

0.43

80

 

Ligands (≥ 10)

8.21

0.90

24

Acceptor

Molecules

3.35

0.05

2,184

 

Ligands

5.87

0.09

2,176

 

Ligands (≤ 3)

5.74

0.09

2,072

 

Ligands (4-9)

7.69

0.53

80

 

Ligands (≥ 10)

11.00

1.18

24

AlogP98

Molecules

2.87

0.05

2,184

 

Ligands

0.81

0.06

2,176

 

Ligands (≤ 3)

0.92

0.06

2,072

 

Ligands (4-9)

-1.33

0.25

80

 

Ligands (≥ 10)

-1.80

0.38

24

LogP

Molecules

0.77

0.08

2,184

 

Ligands

-2.27

0.10

2,176

 

Ligands (≤ 3)

-2.10

0.10

2,072

 

Ligands (4-9)

-5.06

0.50

80

 

Ligands (≥ 10)

-8.11

0.96

24

RotBond

Molecules

4.88

0.09

2,184

 

Ligands

7.49

0.11

2,176

 

Ligands (≤ 3)

7.43

0.11

2072

 

Ligands (4-9)

8.00

0.50

80

 

Ligands (≥ 10)

11.33

1.19

24

  1. * PSA, polar molecular surface area; Donor, H-bond donor counts; Acceptor, H-bond acceptor counts; AlogP98, log of the partition coefficient, atom-type value, using latest parameters; LogP, log of the partition coefficient; RotBond, number of rotatable bonds. †Molecules, ACD-SC-derived ordinary molecules; Ligands, sc-PDB-derived ligands; Ligands (≤ 3), ligands covering ≤ 3 folds; Ligands (4-9), ligands covering 4-9 folds; Ligands (≥ 10), ligands covering ≥ 10 folds.