Chlorine in PDB 6s40: Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites

The structure of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites, PDB code: 6s40 was solved by S.Leysen, X.Guillory, M.Wolter, S.Genet, B.Somsen, J.Patel, P.Castaldi, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.04 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.090, 112.115, 62.604, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.7

The structure of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Calcium	(Ca)	1 atom

The binding sites of Chlorine atom in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites (pdb code 6s40). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites, PDB code: 6s40:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:0.5 occ:1.00 CD A:LYS87 3.8 21.7 0.5 CB A:LYS87 4.0 15.9 0.5 CB A:LYS87 4.0 15.0 0.5 CA A:TYR84 4.1 11.5 1.0 O A:GLU83 4.2 11.3 1.0 CD1 A:TYR84 4.2 11.5 1.0 C A:GLU83 4.3 11.5 1.0 N A:TYR84 4.3 10.4 1.0 CG A:LYS87 4.3 18.5 0.5 CG A:LYS87 4.4 16.9 0.5 CB A:TYR84 4.5 11.9 1.0 O A:HOH462 4.5 22.1 1.0 CB A:GLU83 4.6 11.8 1.0 CD A:LYS87 4.6 19.8 0.5 CG A:TYR84 4.8 10.9 1.0 CE A:LYS87 4.8 24.2 0.5 NZ A:LYS87 4.8 24.9 0.5 CE A:LYS87 5.0 19.8 0.5

Chlorine binding site 2 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl306 b:41.8 occ:0.47 CL A:KTW306 0.0 41.8 0.5 C7 A:KTW306 1.7 36.2 0.5 C1 A:KTW306 1.9 27.4 0.5 C2 A:KTW306 2.5 28.6 0.5 C8 A:KTW306 2.7 38.5 0.5 C3 A:KTW306 2.7 35.9 0.5 S A:KTW306 2.8 31.2 0.5 C A:KTW306 3.1 29.9 0.5 C4 A:KTW306 3.3 35.4 0.5 CG A:GLU39 3.5 19.2 1.0 CB A:GLU39 3.6 16.3 1.0 O A:HOH584 3.6 34.4 1.0 C1 A:KTW308 3.6 66.0 1.0 CA A:GLU39 3.8 12.2 1.0 C3 A:KTW306 3.8 30.2 0.5 C A:KTW306 4.0 39.4 0.5 C2 A:KTW306 4.0 36.9 0.5 CD A:GLU39 4.0 24.4 1.0 C A:KTW308 4.0 64.1 1.0 C8 A:KTW306 4.2 31.9 0.5 C2 A:KTW308 4.3 69.4 1.0 OE2 A:GLU39 4.3 25.0 1.0 C5 A:KTW306 4.4 29.7 0.5 C7 A:KTW306 4.5 31.4 0.5 C1 A:KTW306 4.5 38.4 0.5 N A:GLU39 4.6 11.5 1.0 OE1 A:GLU39 4.6 24.1 1.0 C5 A:KTW306 4.6 33.4 0.5 C4 A:KTW306 4.7 30.4 0.5 O A:HOH437 4.8 20.8 1.0 S A:KTW308 4.9 77.9 1.0 C8 A:KTW308 4.9 73.1 1.0 C A:GLU39 5.0 11.6 1.0

Chlorine binding site 3 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl306 b:34.0 occ:0.53 CL A:KTW306 0.0 34.0 0.5 C7 A:KTW306 1.7 31.4 0.5 C1 A:KTW306 1.8 38.4 0.5 C2 A:KTW306 2.5 36.9 0.5 C8 A:KTW306 2.7 31.9 0.5 C3 A:KTW306 2.7 30.2 0.5 C A:KTW306 2.9 39.4 0.5 S A:KTW306 3.0 35.6 0.5 C4 A:KTW306 3.2 30.4 0.5 OD1 A:ASN42 3.5 17.1 1.0 CL A:KTW308 3.6 88.2 1.0 C3 A:KTW306 3.9 35.9 0.5 C8 A:KTW308 4.0 73.1 1.0 CG A:ASN42 4.0 14.6 1.0 C A:KTW306 4.0 29.9 0.5 C2 A:KTW306 4.0 28.6 0.5 C7 A:KTW308 4.0 73.8 1.0 C8 A:KTW306 4.1 38.5 0.5 O A:HOH563 4.5 29.1 1.0 C7 A:KTW306 4.5 36.2 0.5 O P:HOH414 4.5 42.0 1.0 C1 A:KTW306 4.5 27.4 0.5 C5 A:KTW306 4.6 33.4 0.5 C5 A:KTW306 4.6 29.7 0.5 O A:HOH512 4.6 31.1 1.0 CB A:ASN42 4.6 13.7 1.0 ND2 A:ASN42 4.7 15.6 1.0 O A:HOH414 4.7 28.1 1.0 C4 A:KTW306 4.8 35.4 0.5 C A:KTW308 4.9 64.1 1.0

Chlorine binding site 4 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl307 b:84.0 occ:1.00 CL A:KTW307 0.0 84.0 1.0 C7 A:KTW307 1.7 60.7 1.0 O A:HOH567 2.6 39.7 1.0 C8 A:KTW307 2.7 66.6 1.0 C3 A:KTW307 2.7 54.4 1.0 OD1 A:ASP97 2.7 31.1 1.0 C4 A:KTW307 3.3 49.5 1.0 O A:ASP97 3.4 13.6 1.0 CB A:LEU100 3.5 11.2 1.0 O A:HOH542 3.6 41.4 1.0 CG A:ASP97 3.8 25.4 1.0 CA A:ASP97 3.8 14.4 1.0 N A:GLY101 4.0 12.1 1.0 C A:KTW307 4.0 71.4 1.0 C2 A:KTW307 4.0 56.9 1.0 C A:ASP97 4.1 13.1 1.0 C A:LEU100 4.2 11.2 1.0 CB A:ASP97 4.3 19.4 1.0 CD1 A:LEU100 4.3 11.4 1.0 CA A:LEU100 4.4 10.7 1.0 C1 A:KTW307 4.5 67.1 1.0 CG A:LEU100 4.5 11.7 1.0 CA A:GLY101 4.6 12.7 1.0 C5 A:KTW307 4.6 51.5 1.0 OD2 A:ASP97 4.7 39.0 1.0 O A:LEU100 4.9 10.6 1.0

Chlorine binding site 5 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl308 b:88.2 occ:1.00 CL A:KTW308 0.0 88.2 1.0 C7 A:KTW308 1.7 73.8 1.0 C8 A:KTW308 2.7 73.1 1.0 C3 A:KTW308 2.7 69.8 1.0 C4 A:KTW308 3.2 65.4 1.0 CL A:KTW306 3.6 34.0 0.5 O A:HOH512 3.6 31.1 1.0 S A:KTW306 3.6 35.6 0.5 C4 A:KTW306 3.9 30.4 0.5 C2 A:KTW308 4.0 69.4 1.0 C A:KTW308 4.0 64.1 1.0 C2 A:KTW306 4.0 36.9 0.5 C7 A:KTW306 4.1 31.4 0.5 C3 A:KTW306 4.1 30.2 0.5 C1 A:KTW306 4.3 38.4 0.5 C1 A:KTW308 4.5 66.0 1.0 C5 A:KTW306 4.5 33.4 0.5 C5 A:KTW308 4.6 65.8 1.0 C5 A:KTW306 4.7 29.7 0.5 C3 A:KTW306 4.8 35.9 0.5 O P:HOH414 5.0 42.0 1.0

Chlorine binding site 6 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl309 b:74.1 occ:1.00 CL A:KTW309 0.0 74.1 1.0 C7 A:KTW309 1.7 58.0 1.0 C3 A:KTW309 2.7 57.1 1.0 C8 A:KTW309 2.7 54.5 1.0 C4 A:KTW309 3.2 59.9 1.0 NE A:ARG224 3.7 48.8 1.0 CG A:ARG224 3.9 33.3 1.0 CE1 A:PHE198 3.9 16.2 1.0 C2 A:KTW309 4.0 59.1 1.0 C A:KTW309 4.0 53.4 1.0 CD1 A:PHE198 4.1 15.3 1.0 CZ A:PHE198 4.2 16.6 1.0 CD1 A:LEU227 4.2 19.9 1.0 CG A:PHE198 4.3 15.3 1.0 CD A:ARG224 4.4 40.6 1.0 CE2 A:PHE198 4.4 15.3 1.0 CB A:ARG224 4.5 23.8 1.0 C1 A:KTW309 4.5 56.5 1.0 CD2 A:PHE198 4.5 15.5 1.0 C5 A:KTW309 4.5 70.8 1.0 CA A:ARG224 4.6 20.6 1.0

X.Guillory, M.Wolter, S.Leysen, J.F.Neves, A.Kuusk, S.Genet, B.Somsen, J.Morrow, E.Rivers, L.Van Beek, J.Patel, R.Goodnow, H.Schoenherr, N.Fuller, Q.Cao, R.G.Doveston, L.Brunsveld, M.R.Arkin, M.P.Castaldi, H.Boyd, I.Landrieu, H.Chen, C.Ottmann. Fragment-Based Differential Targeting of Ppi Stabilizer Interfaces. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32501690
DOI: 10.1021/ACS.JMEDCHEM.9B01942