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Table 1 Experimental data for the 54 protein-ligand complexes.

From: Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock

PDB code

Protein

Res (Ã…)

Ligand

Structure Ref.

1AI5

Penicillin acylase

2.4

m-nitrophenylacetic acid

[24]

1AJP

Penicillin acylase

2.3

2,5-dihydroxyphenylacetic acid

[24]

1AMW

Heat shock protein 90

1.9

ADP

[25]

1BGQ

Heat shock protein 90

2.5

radicicol

[26]

1CBR

Retionic acid binding protein

2.9

retinoic acid

[27]

1D3Q

Human thrombin

2.9

benzo [b]thiophene derivative

[28]

1D3T

Human thrombin

3.0

benzo [b]thiophene derivative

[28]

1DWB

a-Thrombin

3.2

benzamidine

[29]

1FLR

Immunoglobulin

1.9

fluorescein

[30]

1GNI

Human serum albumin

2.4

oleic acid

[31]

1HVJ

HIV-1 Protease

2.0

A78791

[32]

1HVR

HIV-1 Protease

1.8

XK263

[33]

1K4G

tRNA-guanine transglycosylase

1.7

quinazoline derivative

[34]

1KV1

p38 MAP kinase

2.5

pyrazol derivative

[35]

1LIF

Adipocyte lipid-binding protein

1.6

stearic acid

[36]

1M0N

Dialkylglycine decarboxylase

2.2

1-aminocyclo-pentanephosphonate

[37]

1M0Q

Dialkylglycine decarboxylase

2.0

S-1-amino-ethanephosphonate

[37]

1OLU

Branched-chain alpha-ketoacid dehydrogenase kinase

1.9

thiamin diphosphate

[38]

1Q8T

cAMP-dependent protein kinase

2.0

(R)-trans-4-(1-aminoethyl)-n-(4-pyridyl) cyclohexanecarboxamide

[39]

1RBP

Retinol-binding protein

2.0

retinol

[40]

1S39

tRNA-guanine transglycosylase

2.0

2-aminoquinazolin-4(3H)-one

[41]

1U33

Alpha-amylase

2.0

5-trihydroxy-6-hydroxymethyl-piperidin-2-one

[42]

1ULB

Purine nucleoside phosphorylase

2.8

guanine

[43]

1UWT

Beta-glycosidase

2.0

D-galactohydroximo-1,5-lactam

[44]

1X8R

3-Phosphoshikimate 1-carboxyvinyltransferase

1.5

phosphonate analogue

[45]

1XD1

Alpha-amylase

2.2

acarbose derived hexasaccharide

[46]

1YDT

cAMP-dependent protein kinase

2.3

n-[2-(4-bromocinnamylamino)ethyl]-5-isoquinoline

[47]

1ZC9

Dialkylglycine decarboxylase

2.0

pyridoxamine 5-phosphate

[48]

2ACK

Acetylcholinesterase

2.4

edrophonium ion

[49]

2BAJ

p38alpha Map kinase

2.3

pyrazol derivative

[50]

2BAK

p38alpha Map kinase

2.2

nicotinamid derivative

[50]

2CEQ

Beta-glycosidase

2.1

glucoimidazole

[51]

2CET

Beta-glycosidase

2.0

phenethyl-substituted glucoimidazole

[51]

2CGR

Immunoglobulin

2.2

N-trisubstituted guanidine

[52]

2CPP

Cytochrome P-450cam

1.6

camphor

[53]

2D3U

RNA-dependent RNA polymerase

2.0

non-nucleoside analogue inhibitor I

[54]

2D3Z

RNA-dependent RNA polymerase

1.8

non-nucleoside analogue inhibitor II

[54]

2FDP

Beta-secretase

2.5

amino-ethylene inhibitor

[55]

2G94

Beta-secretase

1.9

valinamide derivative

[56]

2GBP

D-galactose/D-glucose binding protein

1.9

glucose

[57]

2IFB

Fatty-acid-binding protein

2.0

palmitic acid

[58]

2IWX

Heat shock protein 82

1.5

synthetic macrolactone

[59]

2J77

Beta-glycosidase

2.1

deoxynojirimycin

[Gloster, to be published]

2J78

Beta-glycosidase

1.7

gluco-hydroximolactam

[Gloster, to be published]

2QFU

3-Phosphoshikimate 1-carboxyvinyltransferase

1.6

shikimate-3-phosphate

[60]

2QWB

Neuraminidase

2.0

sialic acid

[61]

2QWD

Neuraminidase

2.0

4-amino-Neu5Ac2en

[61]

2R04

Rhinovirus 14 coat protein

3.0

W71, antiviral agent

[62]

2XIS

Xylose isomerase

1.6

D-xylitol

[63]

2YPI

Triose phosphate isomerase

2.5

2-phosphoglycolic acid

[64]

3PTB

b-Trypsin

1.8

benzamidine

[65]

4HMG

Hemagglutinin

3.0

sialic acid

[66]

7ABP

Arabinose-binding protein

1.7

fucose

[67]