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Table 1 Descriptors of chemical space consisting of sc-PDB-derived ligands and ACD-SC-derived ordinary molecules and corresponding loadings (Varimax normalized) for the first two factors*

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

Descriptors

Characterization

Factor loadings

Software

  

1

2

 

AREA

Total molecular surface area

0.974

0.103

Sybyl

PSA

Polar molecular surface area

0.255

0.892

 

PV

Polar molecular volume

0.501

0.741

 

VOL

Total molecular volume

0.991

0.062

 

MOLWEIGHT

Molecular weight

0.958

0.206

 

Acceptor

H-bond acceptor counts

0.464

0.799

 

Donor

H-bond donor counts

0.376

0.817

 

BondCount

Total bond counts

0.972

0.060

 

Chiral

Counts of chiral center

0.367

0.617

 

Hydrophobe

Hydrophobic fragment counts

0.767

-0.417

 

RingCount

Ring counts

0.686

-0.069

 

RotBonds

Number of rotatable bonds

0.630

0.428

 

HeavyAtoms

Number of non-H atoms

0.978

0.149

 

Carbons

Number of carbons atoms

0.943

-0.228

Perl

Oxygens

Number of oxygen atoms

0.425

0.793

 

Nitrogens

Number of nitrogen atoms

0.475

0.324

 

Sulfurs

Number of sulfur atoms

0.141

-0.009

 

Phosphorus

Number of phosphorus atoms

0.162

0.617

 

Halides

Number of halide atoms

0.076

-0.170

 

DoubleBonds

Number of double bonds

0.527

0.378

 

TripleBonds

Number of triple bonds

-0.009

-0.109

 

RadOfGyration

Radius of gyration

0.888

0.004

Cerius 2

ShadowXY

Surface area projections

0.967

0.076

 

ShadowXZ

 

0.951

0.053

 

ShadowYZ

 

0.877

0.093

 

ShadowXYfrac

 

-0.610

-0.027

 

ShadowXZfrac

 

-0.421

-0.002

 

ShadowYZfrac

 

-0.289

0.039

 

Shadownu

 

0.268

-0.117

 

ShadowXlength

 

0.849

-0.008

 

ShadowYlength

 

0.798

0.075

 

ShadowZlength

 

0.756

0.059

 

Density

Density

-0.089

0.354

 

PMImag

Principal moment of inertia

0.819

0.134

 

AlogP

Log of the partition coefficient using Ghose and Crippen's method.

0.425

-0.727

 

AlogP98

Log of the partition coefficient, atom-type value, using latest parameters.

0.365

-0.852

 

Fh2o

Desolvation free energy for water

-0.479

-0.762

 

Foct

Desolvation free energy for octanol

-0.578

-0.617

 

LogP

Log of the partition coefficient.

-0.022

-0.892

 

MR

Molar refractivity using Hopfinger's method.

0.835

-0.110

 

MolRef

Molar refractivity using linear additive method based on AlogP atom types

0.986

-0.033

 

JX

Balaban indices

-0.567

0.027

 

Kappa1

Kappa topological indices

0.969

0.189

 

Kappa2

 

0.926

0.026

 

Kappa3

 

0.691

0.033

 

Kappa1AM

 

0.958

0.220

 

Kappa2AM

 

0.901

0.050

 

Kappa3AM

 

0.630

0.046

 

PHI

Molecular flexibility index

0.800

0.078

 

SC0

Subgraph topological counts

0.980

0.147

 

SC1

 

0.973

0.125

 

SC2

 

0.943

0.186

 

SC3P

 

0.904

0.141

 

SC3C

 

0.749

0.389

 

SC3CH

 

0.016

-0.086

 

CHI0

Kier and Hall Chi connectivity indices

0.974

0.190

 

CHI1

 

0.983

0.115

 

CHI2

 

0.958

0.210

 

CHI3P

 

0.939

0.136

 

CHI3C

 

0.655

0.484

 

CHI3CH

 

0.015

-0.087

 

CHIV0

 

0.990

0.076

 

CHIV1

 

0.971

0.120

 

CHIV2

 

0.913

0.137

 

CHIV3P

 

0.838

0.096

 

CHIV3C

 

0.476

0.148

 

CHIV3CH

 

0.016

-0.088

 

Wiener

Wiener topological index

0.854

0.186

 

logZ

Logarithm of Hosoya topological index

-0.220

-0.131

 

Zagreb

Zagreb topological index

0.958

0.162

 
  1. *The first factor explains 52.8% of the variance and the second explains 12.7%. Factors with high loadings (>0.9 for first factors and >0.8 for second factors) are shown in bold.