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Table 3 Binding interaction distances and amino acid residues types between the designed ligands and the protease

From: Chemoinformatic design and profiling of some derivatives of 1, 2, 4-oxadiazole as potential dengue virus NS-5 inhibitors

Inhibitor-ligand protease complex

Amino acid residue

Distance (Å)

Type

Binding affinity

34a vs. 5K5M

A:SER763

A:CYS780

:A:SER885

A:ARG773

A:TYR882

A:ASN777

A:TRP833

A:TRP833

A:TYR882

A:HIE786

A:CYS780

A:MET809

1.852

1.799

2.084

2.895

5.199

2.668

3.466

3.867

5.027

4.683

4.011

4.448

C HB

C HB

C HB

C–H-B

Pi–Sulfur

Pi–Lone pair

Pi–Pi stacked

Pi–Pi stacked

Pi–Pi T-shaped

Pi-Alkyl

Pi-Alkyl

Pi-Alkyl

 − 26.54

34b vs. 5K5M

A: ASN777

A: TRP833

A: SER885

A: SER885

A: MET809

A: MET809

A: CYS780

A: TYR882

A: ASN777

A: TRP833

A: TRP833

A: TYR882

A: HIE786

1.858

2.164

1.836

2.123

2.957

2.689

5.877

5.828

2.929

3.565

3.616

4.507

4.157

C HB

C HB

C HB

C HB

Pi–donor hydrogen bond

Pi–Sigma

Pi–Sulfur

Pi–Sulfur

Pi–Lone pair

Pi–Pi stacked

Pi–Pi stacked

Pi–Pi stacked

Pi–alkyl

 − 29.612

34c vs. 5K5M

A:MET809

A:TRP833

A:MET809

A:MET809

A:CYS780

A:TYR882

A:ASN777

A:TRP833

A:TRP833

A:TYR882

A:HIE786

2.370

2.398

2.978

2.669

5.598

5.860

2.797

3.663

3.755

4.385

4.124

C HB

C HB

Pi–donor hydrogen bond

Pi–sigma

Pi–sulfur

Pi–sulfur

Pi–lone pair

Pi–Pi stacked

Pi–Pi stacked

Pi–Pi stacked

Pi–alkyl

 − 22.652

34d vs. 5K5M

A: SER763

A: ARG773

A: SER763

A: TYR882

A: ASN777

A: TRP833

A: TRP833

TYR882

A: HIE786

A: CYS780

A: MET809

2.613

2.649

2.251

5.651

2.904

3.524

4.114

4.621

4.352

4.005

4.361

C HB

C HB

C HB

Pi-Sulfur

Pi-Lone Pair

Pi-Pi Stacked

Pi-Pi Stacked

Pi-Pi T-shaped

Pi-Alkyl

Pi-Alkyl

Pi-Alkyl

 − 23.644

34e vs. 5K5M

A:SER763

A:SER763

A:ARG773

A:TYR882

A:ASN777

A:TRP833

A:TRP833

A:TYR882

A:HIE786

A:CYS780

A:MET809

2.609

2.255

2.676

5.643

2.907

3.520

4.111

4.621

4.343

4.002

4.364

C HB

C HB

C HB

Pi–sulfur

Pi–lone pair

Pi–Pi stacked

Pi–Pi stacked

Pi–Pi T-shaped

Pi–alkyl

Pi–alkyl

Pi–alkyl

 − 23.594

34f vs. 5K5M

A: SER763

A: CYS780

A: TRP833

A: ASP808

: RES1:H9 -RES1:N1

: TYR882

A: ASN777

A: TRP833

A: TRP833

A: TYR882

A: HIE786

A: CYS780

A: MET809

1.993

1.752

1.733

2.548

2.123

5.320

2.864

3.345

3.786

4.970

4.575

3.966

4.371

C HB

C HB

C HB

C HB

C–H-B

Pi–sulfur

Pi–lone pair

Pi–Pi stacked

Pi–Pi stacked

Pi–Pi T-shaped

Pi–alkyl

Pi–alkyl

Pi–alkyl

 − 19.992

34 g vs. 5K5M

A:SER763

A:ASN777

A:CYS780

A:SER885

A:SER885

A:CYS780

A:TYR882

A:ASN777

A:TRP833

A:TRP833

A:TYR882

A:HIE786

A:MET809

2.041

1.582

1.762

1.937

2.832

2.457

5.305

2.727

3.498

3.904

4.892

4.589

4.436

C HB

C HB

C HB

C HB

C–H-B

Pi–donor hydrogen bond

Pi–sulfur

Pi–lone pair

Pi–Pi stacked

Pi–Pi stacked

Pi–Pi T-shaped

Pi–alkyl

Pi–alkyl

 − 23.943

34 h vs. 5K5M

A: ASN777

A: TRP833

A: ASN777

A: SER885

A: MET809

A: CYS780

A: TYR882

A: ASN777

A: TYR882

A: TRP833

A: HIE786

A: MET809

A: ALA776

1.709

2.161

3.071

2.603

2.841

5.257

5.644

2.633

4.454

4.704

4.215

5.252

5.068

C HB

C HB

C HB

C HB

Pi–donor hydrogen bond

Pi–sulfur

Pi–sulfur

Pi–lone pair

Pi–Pi stacked

Pi–Pi T-shaped

Pi–alkyl

Pi–alkyl

Pi–alkyl

 − 19.292

34i vs. 5K5M

A:SER763

A:CYS780

A:TRP833

A:ASP808

:RES1:H9-RES1:N1

A:TYR882

A:ASN777

A:TRP833

A:TRP833

A:TYR882

A:HIE786

A:CYS780

A:MET809

1.987

1.738

1.735

2.545

2.119

5.321

2.869

3.338

3.784

4.978

4.548

3.968

4.369

C HB

C HB

C HB

C HB

C–H-B

Pi–sulfur

Pi–lone pair

Pi–Pi stacked

Pi–Pi stacked

Pi–Pi T-shaped

Pi–alkyl

Pi–alkyl

Pi–alkyl

 − 20.121

34j vs. 5K5M

A: CYS780

A: TRP833

A: ASP808

: RES1:H9 -RES1:N1

A: TYR882

A: ASN777

A: TRP833

A: TRP833

A: TYR882

A: HIE786

A: CYS780

A: MET809

1.738

1.735

2.545

2.119

5.322

2.869

3.338

3.7845

4.978

4.549

3.968

4.3692

C HB

C HB

C HB

C–H-B

Pi–sulfur

Pi–lone pair

Pi–Pi stacked

Pi–Pi stacked

Pi–Pi T-shaped

Pi–alkyl

Pi–alkyl

Pi–alkyl

 − 19.091

Co-crystalised ligand vs. 5K5M

A: ARG729

A: THR794

A: TRP795

A: LYS800

A: GLU802

A: THR794

A: SER710

A: CYS709

A: ARG729

A: THR794

A: HIS711

A: LEU512

A: ALA799

3.109

2.748

3.399

2.823

2.673

3.336

3.574

3.492

4.150

4.035

5.183

4.182

4.224

C HB

C HB

C HB

C HB

C HB

C–H-B

C–H-B

C–H-B

Pi–cation

Pi–donor hydrogen bond

Pi–Pi T-shaped

Alkyl

Alkyl

 − 25.0433

Ribavirin vs. 5K5M

A: LYS756

A: SER763

A: CYS780

A: CYS780

A: ASN777

A: GLN760

A: GLN760

A: THR806

A: THR806

A: SER785

A: THR806

A: GLU807

A: GLN760

A: MET809

A: CYS780

A: MET809

1.690

1.853

2.536

2.467

2.799

2.896

2.208

2.554

2.927

2.194

2.056

2.985

2.477

3.115

4.584

4.758

C HB

C HB

C HB

C HB

C HB

C HB

C HB

C HB

C–H-B

C–H-B

C–H-B

C–H-B

C–H-B

Pi–donor hydrogen bond

Pi–alkyl

Pi–alkyl

 − 12.4462

SAH vs. 5K5M

A:LYS756

A:ASN777

A:CYS780

A:MET809

:GLN760

A:GLN760

A:SER763

A:ASP808

A:GLN760

A:SER785

A:THR806

A:ASP808

A:HIE786

A:TYR882

A:HIE786

2.325

1.871

1.840

2.925

2.099

2.047

2.816

2.398

2.333

2.841

2.385

2.721

2.553

4.328

4.782

C HB

C HB

C HB

C HB

C HB

C HB

C–H-B

C–H-B

C–H-B

C–H-B

C–H-B

C–H-B

C–H-B

Pi–sulfur

Pi–Pi T-shaped

 − 16.5362

  1. C HB conventional hydrogen bond, C–H-B = Carbon hydrogen bond, HB hydrogen bond