Chlorine in PDB 5krt: Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor

The structure of Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor, PDB code: 5krt was solved by D.Patel, J.D.Bauman, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.24 / 1.65
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.069, 72.069, 66.348, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 19.5

The structure of Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Chlorine atom in the Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor (pdb code 5krt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor, PDB code: 5krt:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric 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 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:48.6 occ:1.00 CL1 A:6W6301 0.0 48.6 1.0 C07 A:6W6301 1.8 38.8 1.0 HD2 A:LYS186 2.8 74.7 1.0 N06 A:6W6301 2.8 41.4 1.0 C09 A:6W6301 2.8 35.0 1.0 H091 A:6W6301 3.1 42.0 1.0 C05 A:6W6301 3.2 47.5 1.0 HG23 A:ILE182 3.3 27.6 1.0 HZ2 A:LYS186 3.5 1.0 1.0 CD A:LYS186 3.7 62.2 1.0 C13 A:6W6301 3.8 47.6 1.0 HE3 A:LYS186 3.9 91.2 1.0 H131 A:6W6301 3.9 57.2 1.0 C11 A:6W6301 4.0 45.0 1.0 C10 A:6W6301 4.0 39.9 1.0 HG21 A:ILE182 4.0 27.6 1.0 CG2 A:ILE182 4.0 23.0 1.0 C04 A:6W6301 4.0 54.5 1.0 HB2 A:LYS186 4.1 40.1 1.0 O A:HOH475 4.1 38.5 1.0 CE A:LYS186 4.1 76.0 1.0 HD3 A:LYS186 4.1 74.7 1.0 O03 A:6W6301 4.2 37.3 1.0 NZ A:LYS186 4.2 87.5 1.0 HG22 A:ILE182 4.4 27.6 1.0 C02 A:6W6301 4.5 50.8 1.0 CG A:LYS186 4.7 45.7 1.0 HZ3 A:LYS186 4.7 1.0 1.0 HG3 A:LYS186 4.7 54.8 1.0 HZ1 A:LYS186 4.8 1.0 1.0 HG12 A:ILE182 4.8 24.3 1.0 C14 A:6W6301 4.8 55.1 1.0 CB A:LYS186 4.8 33.4 1.0 H101 A:6W6301 4.9 47.8 1.0

Chlorine binding site 2 out of 4 in the Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric 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 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:61.2 occ:1.00 CL2 A:6W6301 0.0 61.2 1.0 C11 A:6W6301 1.8 45.0 1.0 OE1 A:GLN164 2.7 1.0 1.0 N06 A:6W6301 2.8 41.4 1.0 C10 A:6W6301 2.8 39.9 1.0 HA A:ILE161 2.9 32.5 1.0 HG23 A:ILE161 2.9 28.7 1.0 HG12 A:ILE161 3.0 33.9 1.0 HB2 A:GLN164 3.0 56.6 1.0 H101 A:6W6301 3.1 47.8 1.0 C05 A:6W6301 3.3 47.5 1.0 CD A:GLN164 3.3 94.0 1.0 HB3 A:GLN164 3.4 56.6 1.0 CB A:GLN164 3.6 47.2 1.0 O03 A:6W6301 3.7 37.3 1.0 C04 A:6W6301 3.8 54.5 1.0 CA A:ILE161 3.8 27.1 1.0 CG2 A:ILE161 3.8 23.9 1.0 CG1 A:ILE161 3.9 28.3 1.0 C02 A:6W6301 3.9 50.8 1.0 CG A:GLN164 4.0 72.8 1.0 C07 A:6W6301 4.0 38.8 1.0 C09 A:6W6301 4.0 35.0 1.0 HG21 A:ILE182 4.0 27.6 1.0 CB A:ILE161 4.1 25.1 1.0 NE2 A:GLN164 4.1 0.2 1.0 HE22 A:GLN164 4.2 0.6 1.0 C13 A:6W6301 4.2 47.6 1.0 HG2 A:GLN164 4.3 87.4 1.0 HG13 A:ILE161 4.3 33.9 1.0 HG13 A:VAL165 4.4 47.4 1.0 HG22 A:ILE161 4.4 28.7 1.0 HG21 A:ILE161 4.4 28.7 1.0 HD13 A:ILE182 4.5 27.2 1.0 O A:ILE161 4.5 26.6 1.0 H131 A:6W6301 4.5 57.2 1.0 HG2 A:LYS160 4.6 85.2 1.0 C A:ILE161 4.7 25.9 1.0 N A:ILE161 4.7 29.7 1.0 HE21 A:GLN164 4.7 0.6 1.0 HG3 A:GLN164 4.8 87.4 1.0 O01 A:6W6301 4.8 53.1 1.0 O A:LYS160 4.9 31.1 1.0 HD13 A:ILE161 4.9 38.4 1.0 H091 A:6W6301 4.9 42.0 1.0 HE3 A:LYS160 4.9 0.3 1.0 CD1 A:ILE161 5.0 32.0 1.0 CG2 A:ILE182 5.0 23.0 1.0 S15 A:6W6301 5.0 56.4 1.0 CA A:GLN164 5.0 36.5 1.0 H A:GLN164 5.0 39.9 1.0

Chlorine binding site 3 out of 4 in the Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric 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 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:35.0 occ:1.00 CL1 A:6W6302 0.0 35.0 1.0 C07 A:6W6302 1.8 32.2 1.0 N06 A:6W6302 2.7 32.5 1.0 HD12 A:LEU102 2.8 19.3 0.5 C09 A:6W6302 2.9 35.5 1.0 HA A:TYR99 2.9 19.5 1.0 H131 A:6W6302 3.1 51.7 1.0 C05 A:6W6302 3.1 36.6 1.0 H091 A:6W6302 3.1 42.6 1.0 C13 A:6W6302 3.3 43.1 1.0 HB1 A:ALA98 3.3 19.3 1.0 HD11 A:LEU102 3.4 19.3 0.5 HB3 A:ALA98 3.4 19.3 1.0 N A:TYR99 3.5 15.4 1.0 HB2 A:TYR99 3.5 20.6 1.0 HD1 A:TYR99 3.5 21.1 1.0 CD1 A:LEU102 3.5 16.1 0.5 CA A:TYR99 3.5 16.3 1.0 C A:ALA98 3.7 14.9 1.0 H A:TYR99 3.8 18.5 1.0 CB A:ALA98 3.8 16.1 1.0 HD22 A:LEU102 3.8 20.4 0.5 O A:ALA98 3.9 14.9 1.0 HG A:LEU102 3.9 19.9 0.5 C11 A:6W6302 3.9 35.2 1.0 C10 A:6W6302 4.0 37.4 1.0 CB A:TYR99 4.0 17.2 1.0 HB2 A:ALA129 4.0 18.0 1.0 HD23 A:LEU102 4.1 20.4 0.5 C04 A:6W6302 4.2 40.5 1.0 HD13 A:LEU102 4.3 19.3 0.5 CG A:LEU102 4.3 16.6 0.5 CD1 A:TYR99 4.3 17.6 1.0 HG22 A:THR125 4.4 28.8 1.0 HB2 A:LEU102 4.4 19.4 0.5 CA A:ALA98 4.4 15.0 1.0 C14 A:6W6302 4.4 52.3 1.0 CD2 A:LEU102 4.4 17.0 0.5 O A:GLN95 4.5 19.5 1.0 HB3 A:LEU102 4.5 19.4 0.5 HB2 A:LEU102 4.5 19.5 0.5 HB2 A:ALA98 4.6 19.3 1.0 CG A:TYR99 4.7 17.7 1.0 HG23 A:THR125 4.8 28.8 1.0 HB3 A:TYR99 4.8 20.6 1.0 H101 A:6W6302 4.9 44.9 1.0 CB A:LEU102 4.9 16.2 0.5 C A:TYR99 4.9 16.7 1.0 CB A:ALA129 4.9 15.0 1.0 CG2 A:THR125 4.9 24.0 1.0 HG21 A:THR125 4.9 28.8 1.0 HB1 A:ALA129 4.9 18.0 1.0 O03 A:6W6302 4.9 31.3 1.0 HA A:ALA98 5.0 17.9 1.0 H141 A:6W6302 5.0 62.8 1.0

Chlorine binding site 4 out of 4 in the Hiv-1 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric 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 Integrase Catalytic Core Domain (Ccd) in Complex with A Fragment-Derived Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:41.7 occ:1.00 CL2 A:6W6302 0.0 41.7 1.0 C11 A:6W6302 1.8 35.2 1.0 N06 A:6W6302 2.8 32.5 1.0 C10 A:6W6302 2.9 37.4 1.0 H101 A:6W6302 3.1 44.9 1.0 C05 A:6W6302 3.3 36.6 1.0 C02 A:6W6302 3.3 36.0 1.0 HE21 A:GLN95 3.3 78.7 1.0 HG23 A:THR125 3.4 28.8 1.0 O03 A:6W6302 3.4 31.3 1.0 C04 A:6W6302 3.5 40.5 1.0 NE2 A:GLN95 3.7 65.6 1.0 O01 A:6W6302 3.8 37.0 1.0 HG21 A:THR125 3.8 28.8 1.0 HE22 A:GLN95 3.9 78.7 1.0 C07 A:6W6302 4.0 32.2 1.0 C09 A:6W6302 4.0 35.5 1.0 CG2 A:THR125 4.1 24.0 1.0 HG2 A:GLN95 4.2 49.2 1.0 C13 A:6W6302 4.5 43.1 1.0 HG1 A:THR125 4.5 35.7 1.0 CD A:GLN95 4.5 57.3 1.0 O A:HOH506 4.7 51.7 1.0 OG1 A:THR125 4.7 29.8 1.0 HG22 A:THR125 4.7 28.8 1.0 CG A:GLN95 4.8 41.0 1.0 S15 A:6W6302 4.9 47.2 1.0 H091 A:6W6302 4.9 42.6 1.0 H131 A:6W6302 4.9 51.7 1.0 O A:HOH478 5.0 52.1 1.0

D.Patel, J.Antwi, P.C.Koneru, E.Serrao, S.Forli, J.J.Kessl, L.Feng, N.Deng, R.M.Levy, J.R.Fuchs, A.J.Olson, A.N.Engelman, J.D.Bauman, M.Kvaratskhelia, E.Arnold. A New Class of Allosteric Hiv-1 Integrase Inhibitors Identified By Crystallographic Fragment Screening of the Catalytic Core Domain. J.Biol.Chem. V. 291 23569 2016.
ISSN: ESSN 1083-351X
PubMed: 27645997
DOI: 10.1074/JBC.M116.753384