Chlorine in PDB 4djo: Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56

The structure of Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56, PDB code: 4djo was solved by C.A.Schiffer, M.N.L.Nalam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.20 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.732, 57.763, 61.736, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 21.7

The binding sites of Chlorine atom in the Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56 (pdb code 4djo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56, PDB code: 4djo:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56


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 Wild-Type Hiv-1 Protease in Complex with MKP56 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:36.3 occ:0.34 CL2 A:MK5101 0.0 36.3 0.3 CL2 A:MK5101 1.0 39.8 0.3 C28 A:MK5101 1.3 35.7 0.3 C28 A:MK5101 1.7 33.8 0.3 C28 A:MK5101 1.8 33.8 0.3 CL1 A:MK5101 1.9 38.2 0.3 C26 A:MK5101 2.1 33.2 0.3 N25 A:MK5101 2.2 30.2 0.3 CL1 A:MK5101 2.3 37.0 0.3 C26 A:MK5101 2.8 31.7 0.3 C26 A:MK5101 2.8 31.8 0.3 N25 A:MK5101 2.9 28.2 0.3 CL1 A:MK5101 2.9 37.8 0.3 CL2 A:MK5101 3.0 37.5 0.3 N25 A:MK5101 3.0 28.1 0.3 O A:GLY48 3.1 24.4 1.0 O A:HOH221 3.3 34.1 1.0 O A:HOH223 3.3 36.0 1.0 O27 A:MK5101 3.3 31.6 0.3 C24 A:MK5101 3.7 27.9 0.3 C A:GLY48 3.7 24.7 1.0 O27 A:MK5101 3.9 30.7 0.3 O27 A:MK5101 4.0 30.8 0.3 CA A:GLY48 4.0 23.9 1.0 N A:GLY48 4.1 23.2 1.0 C24 A:MK5101 4.3 27.6 0.3 C24 A:MK5101 4.5 27.6 0.3 C23 A:MK5101 4.5 26.0 0.3 C34 A:MK5101 4.6 29.3 0.3 C34 A:MK5101 4.6 29.2 0.3 C34 A:MK5101 4.6 29.3 0.3 O B:HOH227 4.6 39.1 1.0 CD1 A:ILE47 4.7 33.1 0.5 CG1 A:ILE47 4.7 29.9 0.5 N A:GLY49 4.7 25.0 1.0 C35 A:MK5101 4.9 29.6 0.3 C35 A:MK5101 4.9 29.5 0.3 C35 A:MK5101 4.9 29.6 0.3 O23 A:MK5101 4.9 24.4 0.3 O23 A:MK5101 5.0 24.5 0.3 OD2 A:ASP29 5.0 27.1 1.0 O A:HOH229 5.0 44.1 1.0 O23 A:MK5101 5.0 25.0 0.3

Chlorine binding site 2 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56


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 Wild-Type Hiv-1 Protease in Complex with MKP56 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:37.5 occ:0.33 CL2 A:MK5101 0.0 37.5 0.3 CL1 A:MK5101 0.1 37.8 0.3 O27 A:MK5101 1.3 31.6 0.3 C26 A:MK5101 1.5 33.2 0.3 C28 A:MK5101 1.7 35.7 0.3 C28 A:MK5101 1.8 33.8 0.3 C28 A:MK5101 1.8 33.8 0.3 C26 A:MK5101 2.7 31.8 0.3 C26 A:MK5101 2.7 31.7 0.3 N25 A:MK5101 2.9 30.2 0.3 CL1 A:MK5101 2.9 37.0 0.3 CL2 A:MK5101 3.0 36.3 0.3 O A:HOH205 3.0 21.5 1.0 CL1 A:MK5101 3.0 38.2 0.3 O27 A:MK5101 3.0 30.7 0.3 O27 A:MK5101 3.1 30.8 0.3 CL2 A:MK5101 3.3 39.8 0.3 CG A:ASP29 3.4 24.6 1.0 OD2 A:ASP29 3.4 27.1 1.0 OD1 A:ASP29 3.5 23.5 1.0 N25 A:MK5101 3.6 28.2 0.3 N25 A:MK5101 3.7 28.1 0.3 C34 A:MK5101 3.8 29.3 0.3 C34 A:MK5101 3.8 29.2 0.3 C34 A:MK5101 3.8 29.3 0.3 O B:HOH206 3.8 29.8 1.0 C24 A:MK5101 3.9 27.9 0.3 N A:ASP29 3.9 20.1 1.0 NH2 B:ARG8 3.9 32.0 1.0 C33 A:MK5101 4.1 27.6 0.3 C33 A:MK5101 4.1 27.5 0.3 C33 A:MK5101 4.1 27.5 0.3 CB A:ASP29 4.1 22.6 1.0 O A:GLY27 4.1 20.2 1.0 O B:HOH227 4.3 39.1 1.0 NE B:ARG8 4.4 29.6 1.0 O23 A:MK5101 4.4 25.0 0.3 O23 A:MK5101 4.4 24.4 0.3 O23 A:MK5101 4.4 24.5 0.3 CZ B:ARG8 4.5 34.1 1.0 CA A:ASP29 4.6 21.9 1.0 C23 A:MK5101 4.7 26.0 0.3 CA A:ALA28 4.8 19.5 1.0 C24 A:MK5101 4.8 27.6 0.3 C A:ALA28 4.8 19.5 1.0 C35 A:MK5101 4.8 29.6 0.3 C35 A:MK5101 4.8 29.5 0.3 C35 A:MK5101 4.8 29.6 0.3 O A:HOH229 4.8 44.1 1.0 C24 A:MK5101 4.9 27.6 0.3

Chlorine binding site 3 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56


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 Wild-Type Hiv-1 Protease in Complex with MKP56 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:39.8 occ:0.33 CL2 A:MK5101 0.0 39.8 0.3 CL2 A:MK5101 1.0 36.3 0.3 CL1 A:MK5101 1.7 37.0 0.3 C28 A:MK5101 1.8 35.7 0.3 C28 A:MK5101 2.0 33.8 0.3 C28 A:MK5101 2.0 33.8 0.3 O A:HOH221 2.7 34.1 1.0 C26 A:MK5101 2.7 33.2 0.3 CL1 A:MK5101 2.8 38.2 0.3 N25 A:MK5101 2.9 30.2 0.3 O A:HOH223 2.9 36.0 1.0 C26 A:MK5101 3.1 31.8 0.3 C26 A:MK5101 3.2 31.7 0.3 CL1 A:MK5101 3.3 37.8 0.3 CL2 A:MK5101 3.3 37.5 0.3 N25 A:MK5101 3.5 28.2 0.3 N25 A:MK5101 3.6 28.1 0.3 O27 A:MK5101 3.7 31.6 0.3 O A:GLY48 3.9 24.4 1.0 O27 A:MK5101 4.1 30.7 0.3 O27 A:MK5101 4.2 30.8 0.3 N A:GLY48 4.2 23.2 1.0 O A:HOH229 4.2 44.1 1.0 C24 A:MK5101 4.2 27.9 0.3 CD1 A:ILE47 4.3 33.1 0.5 C A:GLY48 4.4 24.7 1.0 CA A:GLY48 4.4 23.9 1.0 OD2 A:ASP29 4.5 27.1 1.0 CG1 A:ILE47 4.6 29.9 0.5 NH2 B:ARG8 4.7 32.0 1.0 O B:HOH227 4.7 39.1 1.0 C24 A:MK5101 4.9 27.6 0.3 C24 A:MK5101 5.0 27.6 0.3

Chlorine binding site 4 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56


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 Wild-Type Hiv-1 Protease in Complex with MKP56 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:37.8 occ:0.34 CL1 A:MK5101 0.0 37.8 0.3 CL2 A:MK5101 0.1 37.5 0.3 O27 A:MK5101 1.3 31.6 0.3 C26 A:MK5101 1.5 33.2 0.3 C28 A:MK5101 1.7 35.7 0.3 C28 A:MK5101 1.8 33.8 0.3 C28 A:MK5101 1.8 33.8 0.3 C26 A:MK5101 2.7 31.8 0.3 C26 A:MK5101 2.7 31.7 0.3 N25 A:MK5101 2.9 30.2 0.3 CL1 A:MK5101 2.9 37.0 0.3 CL2 A:MK5101 2.9 36.3 0.3 CL1 A:MK5101 3.0 38.2 0.3 O A:HOH205 3.0 21.5 1.0 O27 A:MK5101 3.1 30.7 0.3 O27 A:MK5101 3.1 30.8 0.3 CL2 A:MK5101 3.3 39.8 0.3 OD2 A:ASP29 3.4 27.1 1.0 CG A:ASP29 3.4 24.6 1.0 OD1 A:ASP29 3.5 23.5 1.0 N25 A:MK5101 3.6 28.2 0.3 N25 A:MK5101 3.6 28.1 0.3 C34 A:MK5101 3.8 29.3 0.3 C34 A:MK5101 3.8 29.2 0.3 C34 A:MK5101 3.8 29.3 0.3 O B:HOH206 3.8 29.8 1.0 C24 A:MK5101 3.9 27.9 0.3 NH2 B:ARG8 3.9 32.0 1.0 N A:ASP29 3.9 20.1 1.0 C33 A:MK5101 4.1 27.6 0.3 C33 A:MK5101 4.1 27.5 0.3 C33 A:MK5101 4.1 27.5 0.3 CB A:ASP29 4.1 22.6 1.0 O A:GLY27 4.2 20.2 1.0 O B:HOH227 4.2 39.1 1.0 NE B:ARG8 4.4 29.6 1.0 O23 A:MK5101 4.4 25.0 0.3 O23 A:MK5101 4.4 24.4 0.3 O23 A:MK5101 4.4 24.5 0.3 CZ B:ARG8 4.5 34.1 1.0 CA A:ASP29 4.6 21.9 1.0 C23 A:MK5101 4.7 26.0 0.3 C24 A:MK5101 4.8 27.6 0.3 C35 A:MK5101 4.8 29.6 0.3 C35 A:MK5101 4.8 29.5 0.3 C35 A:MK5101 4.8 29.6 0.3 CA A:ALA28 4.8 19.5 1.0 O A:HOH229 4.8 44.1 1.0 C A:ALA28 4.8 19.5 1.0 C24 A:MK5101 4.9 27.6 0.3

Chlorine binding site 5 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:37.0 occ:0.33 CL1 A:MK5101 0.0 37.0 0.3 C28 A:MK5101 1.5 33.8 0.3 CL2 A:MK5101 1.7 39.8 0.3 C28 A:MK5101 1.8 33.8 0.3 C28 A:MK5101 2.3 35.7 0.3 CL2 A:MK5101 2.3 36.3 0.3 C26 A:MK5101 2.5 33.2 0.3 C26 A:MK5101 2.7 31.8 0.3 O A:HOH229 2.7 44.1 1.0 C26 A:MK5101 2.7 31.7 0.3 CL1 A:MK5101 2.9 37.8 0.3 CL2 A:MK5101 2.9 37.5 0.3 N25 A:MK5101 3.0 30.2 0.3 OD2 A:ASP29 3.1 27.1 1.0 O27 A:MK5101 3.1 31.6 0.3 O27 A:MK5101 3.2 30.7 0.3 O27 A:MK5101 3.2 30.8 0.3 N25 A:MK5101 3.6 28.2 0.3 O A:HOH221 3.6 34.1 1.0 N25 A:MK5101 3.7 28.1 0.3 CG A:ASP29 3.7 24.6 1.0 CL1 A:MK5101 3.9 38.2 0.3 CB A:ASP29 4.0 22.6 1.0 NH2 B:ARG8 4.0 32.0 1.0 CD1 A:ILE47 4.0 33.1 0.5 C24 A:MK5101 4.1 27.9 0.3 OD2 A:ASP30 4.3 36.3 1.0 O A:HOH223 4.3 36.0 1.0 OD1 A:ASP29 4.7 23.5 1.0 CG1 A:ILE47 4.7 29.9 0.5 C24 A:MK5101 4.9 27.6 0.3 C24 A:MK5101 4.9 27.6 0.3 O A:GLY48 5.0 24.4 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Wild-Type Hiv-1 Protease in Complex with MKP56 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:38.2 occ:0.33 CL1 A:MK5101 0.0 38.2 0.3 C28 A:MK5101 1.8 35.7 0.3 CL2 A:MK5101 1.9 36.3 0.3 C26 A:MK5101 2.7 33.2 0.3 C28 A:MK5101 2.7 33.8 0.3 CL2 A:MK5101 2.8 39.8 0.3 C34 A:MK5101 2.8 29.3 0.3 C34 A:MK5101 2.8 29.2 0.3 C34 A:MK5101 2.8 29.3 0.3 C35 A:MK5101 2.9 29.6 0.3 C35 A:MK5101 2.9 29.5 0.3 C35 A:MK5101 2.9 29.6 0.3 CL1 A:MK5101 3.0 37.8 0.3 C28 A:MK5101 3.0 33.8 0.3 CL2 A:MK5101 3.0 37.5 0.3 N25 A:MK5101 3.1 30.2 0.3 O A:GLY48 3.4 24.4 1.0 O27 A:MK5101 3.7 31.6 0.3 O B:HOH227 3.7 39.1 1.0 N25 A:MK5101 3.8 28.2 0.3 C26 A:MK5101 3.8 31.7 0.3 C33 A:MK5101 3.8 27.6 0.3 C33 A:MK5101 3.8 27.5 0.3 C33 A:MK5101 3.8 27.5 0.3 C A:GLY48 3.8 24.7 1.0 C26 A:MK5101 3.8 31.8 0.3 N25 A:MK5101 3.9 28.1 0.3 CL1 A:MK5101 3.9 37.0 0.3 O A:HOH223 4.0 36.0 1.0 C36 A:MK5101 4.0 27.4 0.3 C36 A:MK5101 4.0 27.4 0.3 C36 A:MK5101 4.0 27.5 0.3 N A:GLY49 4.3 25.0 1.0 CA A:GLY49 4.4 25.9 1.0 C24 A:MK5101 4.5 27.9 0.3 CA A:GLY48 4.5 23.9 1.0 O A:HOH251 4.6 40.6 1.0 C38 A:MK5101 4.7 25.9 0.3 C38 A:MK5101 4.7 25.8 0.3 C38 A:MK5101 4.7 25.8 0.3 C37 A:MK5101 4.7 26.6 0.3 C37 A:MK5101 4.7 26.5 0.3 C37 A:MK5101 4.7 26.5 0.3 C23 A:MK5101 4.8 26.0 0.3 O23 A:MK5101 4.8 24.4 0.3 O23 A:MK5101 4.8 24.5 0.3 O B:HOH206 4.9 29.8 1.0 O23 A:MK5101 4.9 25.0 0.3 O27 A:MK5101 4.9 30.7 0.3 O A:HOH221 4.9 34.1 1.0 O27 A:MK5101 5.0 30.8 0.3 C A:GLY49 5.0 26.3 1.0

M.K.Parai, D.J.Huggins, H.Cao, M.N.Nalam, A.Ali, C.A.Schiffer, B.Tidor, T.M.Rana. Design, Synthesis, and Biological and Structural Evaluations of Novel Hiv-1 Protease Inhibitors to Combat Drug Resistance. J.Med.Chem. V. 55 6328 2012.
ISSN: ISSN 0022-2623
PubMed: 22708897
DOI: 10.1021/JM300238H