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Chlorine in PDB 4j02: Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid:
2.7.7.48; 3.4.21.98; 3.6.1.15; 3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid, PDB code: 4j02 was solved by R.Coulombe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.760, 108.340, 133.060, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4j02:

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid (pdb code 4j02). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid, PDB code: 4j02:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4j02

Go back to Chlorine Binding Sites List in 4j02
Chlorine binding site 1 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:31.5
occ:1.00
 CL1 A:1JE601 0.0 31.5 1.0
C2 A:1JE601 1.7 27.4 1.0
C3 A:1JE601 2.7 28.8 1.0
C1 A:1JE601 2.7 27.3 1.0
N7 A:1JE601 3.2 25.5 1.0
CD2 A:LEU419 3.7 23.1 1.0
CG1 A:ILE482 3.8 24.7 1.0
CG2 A:ILE482 3.9 23.1 1.0
CD1 A:ILE482 3.9 26.6 1.0
O A:HOH743 3.9 24.2 1.0
CD1 A:LEU419 4.0 20.6 1.0
C4 A:1JE601 4.0 25.7 1.0
C6 A:1JE601 4.1 27.0 1.0
CD1 A:LEU497 4.3 17.9 1.0
O A:HOH1032 4.4 40.0 1.0
CG A:LEU419 4.5 20.7 1.0
CB A:ILE482 4.5 25.0 1.0
C8 A:1JE601 4.5 26.0 1.0
C5 A:1JE601 4.6 27.4 1.0
O18 A:1JE601 4.6 32.3 1.0

Chlorine binding site 2 out of 4 in 4j02

Go back to Chlorine Binding Sites List in 4j02
Chlorine binding site 2 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:31.4
occ:1.00
 CL2 A:1JE601 0.0 31.4 1.0
C5 A:1JE601 1.7 27.4 1.0
C4 A:1JE601 2.7 25.7 1.0
C6 A:1JE601 2.8 27.0 1.0
O A:HOH1042 3.1 29.0 1.0
C9 A:1JE601 3.5 26.0 1.0
C13 A:1JE601 3.5 26.5 1.0
CD A:ARG501 3.6 32.9 1.0
CE A:MET423 3.7 23.1 1.0
CB A:ARG501 3.8 22.8 1.0
CA A:ARG498 3.9 20.7 1.0
NH1 A:ARG501 4.0 39.1 1.0
O A:LEU497 4.0 20.1 1.0
C3 A:1JE601 4.0 28.8 1.0
C1 A:1JE601 4.1 27.3 1.0
N A:ARG498 4.2 19.0 1.0
C A:LEU497 4.2 19.9 1.0
CG A:ARG501 4.2 29.0 1.0
NE A:ARG501 4.4 34.9 1.0
C2 A:1JE601 4.6 27.4 1.0
CZ A:ARG501 4.6 37.6 1.0
CB A:ARG498 4.7 20.5 1.0
CB A:LEU497 4.7 17.7 1.0
C8 A:1JE601 4.7 26.0 1.0
SD A:MET423 4.9 22.1 1.0
C A:ARG498 4.9 20.2 1.0
O A:ARG498 5.0 21.6 1.0
C12 A:1JE601 5.0 27.8 1.0

Chlorine binding site 3 out of 4 in 4j02

Go back to Chlorine Binding Sites List in 4j02
Chlorine binding site 3 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:40.9
occ:1.00
 CL1 B:1JE601 0.0 40.9 1.0
C2 B:1JE601 1.7 37.3 1.0
C1 B:1JE601 2.7 36.9 1.0
C3 B:1JE601 2.7 37.7 1.0
N7 B:1JE601 3.2 35.5 1.0
CD2 B:LEU419 3.8 27.0 1.0
CD1 B:LEU419 4.0 25.8 1.0
CD1 B:LEU497 4.0 29.6 1.0
CD1 B:ILE482 4.0 34.0 1.0
C4 B:1JE601 4.1 38.2 1.0
C6 B:1JE601 4.1 37.3 1.0
O B:HOH1060 4.1 31.3 1.0
CG1 B:ILE482 4.1 32.2 1.0
CG2 B:ILE482 4.2 30.7 1.0
CG B:LEU419 4.5 28.2 1.0
O18 B:1JE601 4.5 36.3 1.0
C8 B:1JE601 4.5 34.7 1.0
O B:HOH1322 4.5 44.0 1.0
C5 B:1JE601 4.6 37.9 1.0
CB B:ILE482 4.8 30.6 1.0

Chlorine binding site 4 out of 4 in 4j02

Go back to Chlorine Binding Sites List in 4j02
Chlorine binding site 4 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:42.1
occ:1.00
 CL2 B:1JE601 0.0 42.1 1.0
C5 B:1JE601 1.7 37.9 1.0
C4 B:1JE601 2.7 38.2 1.0
C6 B:1JE601 2.8 37.3 1.0
C9 B:1JE601 3.4 35.1 1.0
C13 B:1JE601 3.5 34.9 1.0
CE B:MET423 3.8 31.2 1.0
CD B:ARG501 3.8 45.1 1.0
CB B:ARG501 3.9 39.0 1.0
CA B:ARG498 3.9 33.9 1.0
C3 B:1JE601 4.0 37.7 1.0
C1 B:1JE601 4.1 36.9 1.0
O B:LEU497 4.2 31.4 1.0
NH1 B:ARG498 4.2 50.8 1.0
CG B:ARG498 4.3 39.5 1.0
N B:ARG498 4.3 32.3 1.0
C B:LEU497 4.4 30.9 1.0
CG B:ARG501 4.4 41.7 1.0
NH1 B:ARG501 4.6 50.3 1.0
CB B:ARG498 4.6 35.4 1.0
C2 B:1JE601 4.6 37.3 1.0
C8 B:1JE601 4.7 34.7 1.0
O B:ARG498 4.8 31.9 1.0
C B:ARG498 4.8 33.2 1.0
NE B:ARG501 4.9 49.6 1.0
C12 B:1JE601 5.0 34.8 1.0

Reference:

T.A.Stammers, R.Coulombe, J.Rancourt, B.Thavonekham, G.Fazal, S.Goulet, A.Jakalian, D.Wernic, Y.Tsantrizos, M.A.Poupart, M.Bos, G.Mckercher, L.Thauvette, G.Kukolj, P.L.Beaulieu. Discovery of A Novel Series of Non-Nucleoside Thumb Pocket 2 Hcv NS5B Polymerase Inhibitors. Bioorg.Med.Chem.Lett. V. 23 2585 2013.
ISSN: ISSN 0960-894X
PubMed: 23545108
DOI: 10.1016/J.BMCL.2013.02.110
Page generated: Fri Jul 11 17:08:54 2025

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