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Chlorine in PDB 2qnq: Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor

Enzymatic activity of Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor

All present enzymatic activity of Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor, PDB code: 2qnq was solved by J.Boettcher, A.Blum, A.Heine, W.E.Diederich, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.564, 85.903, 46.538, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor (pdb code 2qnq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor, PDB code: 2qnq:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 2qnq

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Chlorine binding site 1 out of 5 in the Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2501

b:30.9
occ:1.00
 CL1 A:QN32501 0.0 30.9 1.0
C17 A:QN32501 1.7 34.9 1.0
C1 A:QN32501 2.7 36.1 1.0
C26 A:QN32501 2.8 35.2 1.0
O41 A:QN32501 3.1 38.8 1.0
CB A:ALA28 3.3 15.3 1.0
S8 A:QN32501 3.4 38.2 1.0
CG2 A:VAL32 3.4 20.4 1.0
O A:ASP30 3.4 14.7 1.0
C7 A:QN32501 3.6 38.2 1.0
N28 A:QN32501 3.6 38.4 1.0
CG2 A:ILE84 3.9 18.9 1.0
C4 A:QN32501 4.1 37.0 1.0
C19 A:QN32501 4.1 34.4 1.0
CA A:ALA28 4.2 18.1 1.0
C A:ASP30 4.3 16.9 1.0
CB A:ILE84 4.5 19.2 1.0
CB A:VAL32 4.6 17.5 1.0
N A:ASP30 4.6 17.6 1.0
CD1 A:ILE84 4.6 23.0 1.0
C23 A:QN32501 4.6 38.5 1.0
C3 A:QN32501 4.6 37.1 1.0
O10 A:QN32501 4.8 38.7 1.0
C A:ALA28 4.8 17.7 1.0
C21 A:QN32501 4.9 37.2 1.0
N A:ASP29 4.9 17.1 1.0
CA A:ASP30 4.9 18.2 1.0
O A:HOH3032 4.9 32.6 1.0
CG1 A:ILE84 4.9 19.2 1.0
C12 A:QN32501 5.0 37.6 1.0
CD1 A:ILE47 5.0 24.3 1.0

Chlorine binding site 2 out of 5 in 2qnq

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Chlorine binding site 2 out of 5 in the Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2501

b:41.0
occ:1.00
 CL3 A:QN32501 0.0 41.0 1.0
C20 A:QN32501 1.7 40.9 1.0
C5 A:QN32501 2.7 39.9 1.0
C27 A:QN32501 2.8 41.0 1.0
O B:GLY48 2.9 22.1 1.0
O11 A:QN32501 3.0 40.9 1.0
CA B:GLY49 3.1 21.9 1.0
C29 A:QN32501 3.4 35.5 1.0
S9 A:QN32501 3.5 41.3 1.0
C31 A:QN32501 3.5 37.6 1.0
C B:GLY48 3.7 21.5 1.0
C B:GLY49 3.9 22.6 1.0
N B:GLY49 3.9 22.1 1.0
C13 A:QN32501 3.9 36.2 1.0
C30 A:QN32501 4.0 35.8 1.0
N B:ILE50 4.0 22.7 1.0
C6 A:QN32501 4.0 39.5 1.0
C18 A:QN32501 4.1 41.7 1.0
C24 A:QN32501 4.1 38.7 1.0
N32 A:QN32501 4.3 39.7 1.0
C12 A:QN32501 4.4 37.6 1.0
C14 A:QN32501 4.4 36.6 1.0
C25 A:QN32501 4.4 38.0 1.0
C2 A:QN32501 4.6 40.9 1.0
O40 A:QN32501 4.6 40.4 1.0
O B:GLY49 4.8 24.3 1.0
CB A:ILE50 4.8 29.5 1.0

Chlorine binding site 3 out of 5 in 2qnq

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Chlorine binding site 3 out of 5 in the Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2602

b:23.0
occ:1.00
 N A:THR74 3.1 19.8 1.0
ND2 A:ASN88 3.3 14.2 1.0
OG1 A:THR74 3.7 21.6 1.0
CB A:THR74 3.7 18.9 1.0
CA A:GLY73 3.7 19.8 1.0
CB A:ASN88 3.9 15.7 1.0
C A:GLY73 3.9 19.6 1.0
O A:HOH3021 4.0 21.1 1.0
CA A:THR74 4.0 19.0 1.0
CG A:ASN88 4.1 16.2 1.0
O A:ASN88 4.5 15.5 1.0
O A:THR74 4.7 17.4 1.0
CA A:ASN88 4.9 16.5 1.0
C A:THR74 4.9 18.2 1.0
C A:ASN88 5.0 16.5 1.0

Chlorine binding site 4 out of 5 in 2qnq

Go back to Chlorine Binding Sites List in 2qnq
Chlorine binding site 4 out of 5 in the Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2601

b:17.4
occ:1.00
 NE1 B:TRP6 3.2 18.7 1.0
O A:HOH3015 3.3 27.0 1.0
CE2 B:TRP6 3.9 18.0 1.0
CZ2 B:TRP6 3.9 15.7 1.0
CG2 B:THR4 4.0 17.5 1.0
CD1 B:TRP6 4.3 19.2 1.0
CB B:THR4 4.8 17.5 1.0

Chlorine binding site 5 out of 5 in 2qnq

Go back to Chlorine Binding Sites List in 2qnq
Chlorine binding site 5 out of 5 in the Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hiv-1 Protease in Complex with A Chloro Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2603

b:25.9
occ:1.00
 O B:HOH3063 2.8 28.5 1.0
N B:THR74 3.3 18.6 1.0
ND2 B:ASN88 3.3 13.7 1.0
CA B:GLY73 3.8 18.7 1.0
OG1 B:THR74 3.9 21.7 1.0
CB B:THR74 3.9 16.8 1.0
CB B:ASN88 4.0 14.8 1.0
C B:GLY73 4.0 18.7 1.0
CG B:ASN88 4.1 17.2 1.0
CA B:THR74 4.2 18.6 1.0
OE1 B:GLN92 4.3 20.4 1.0
O B:HOH3006 4.3 17.7 1.0
O B:ASN88 4.4 20.9 1.0
CD2 B:LEU89 4.7 12.6 1.0
O B:THR74 4.7 17.7 1.0
C B:ASN88 4.8 17.5 1.0
CA B:ASN88 4.9 15.3 1.0
C B:THR74 5.0 18.3 1.0

Reference:

A.Blum, J.Bottcher, A.Heine, G.Klebe, W.E.Diederich. Structure-Guided Design of C2-Symmetric Hiv-1 Protease Inhibitors Based on A Pyrrolidine Scaffold. J.Med.Chem. V. 51 2078 2008.
ISSN: ISSN 0022-2623
PubMed: 18348517
DOI: 10.1021/JM701142S
Page generated: Fri Jul 11 00:15:21 2025

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