Chlorine in PDB 5l7i: Structure of Human Smoothened in Complex with Vismodegib

The structure of Structure of Human Smoothened in Complex with Vismodegib, PDB code: 5l7i was solved by E.X.B.Byrne, R.Sircar, P.S.Miller, G.Hedger, G.Luchetti, S.Nachtergaele, M.D.Tully, L.Mydock-Mcgrane, D.F.Covey, R.F.Rambo, M.S.P.Sansom, S.Newstead, R.Rohatgi, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.32 / 3.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.820, 71.290, 107.020, 91.53, 98.20, 105.92
R / Rfree (%)	24.5 / 25.7

The structure of Structure of Human Smoothened in Complex with Vismodegib also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Structure of Human Smoothened in Complex with Vismodegib (pdb code 5l7i). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Human Smoothened in Complex with Vismodegib, PDB code: 5l7i:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of Human Smoothened in Complex with Vismodegib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Human Smoothened in Complex with Vismodegib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1202 b:0.8 occ:1.00 CL1 A:VIS1202 0.0 0.8 1.0 C11 A:VIS1202 1.7 0.8 1.0 C10 A:VIS1202 2.7 0.8 1.0 C12 A:VIS1202 2.7 1.0 1.0 C14 A:VIS1202 3.1 0.7 1.0 C15 A:VIS1202 3.4 0.7 1.0 CD1 A:LEU522 3.5 96.7 1.0 N1 A:VIS1202 3.9 0.1 1.0 C9 A:VIS1202 4.0 0.3 1.0 C13 A:VIS1202 4.0 0.2 1.0 CB A:SER387 4.1 83.2 1.0 CG A:LEU522 4.1 96.2 1.0 CH2 A:TRP281 4.1 77.0 1.0 CB A:GLU518 4.1 0.1 1.0 CA A:SER387 4.2 81.1 1.0 SD A:MET230 4.3 98.0 1.0 CD2 A:LEU522 4.3 96.7 1.0 CE A:MET230 4.4 95.7 1.0 CZ3 A:TRP281 4.4 76.4 1.0 C16 A:VIS1202 4.4 0.1 1.0 O A:GLU518 4.5 0.4 1.0 C8 A:VIS1202 4.5 0.1 1.0 CD1 A:ILE234 4.6 91.0 1.0 CG A:MET230 4.8 93.5 1.0 C18 A:VIS1202 4.8 0.2 1.0 N A:SER387 4.8 82.0 1.0 OE1 A:GLU518 4.9 0.4 1.0 C A:GLU518 4.9 0.1 1.0 CG A:GLU518 4.9 0.5 1.0

Chlorine binding site 2 out of 4 in the Structure of Human Smoothened in Complex with Vismodegib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Human Smoothened in Complex with Vismodegib within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1202 b:0.3 occ:1.00 CL A:VIS1202 0.0 0.3 1.0 C5 A:VIS1202 1.7 0.5 1.0 C6 A:VIS1202 2.7 0.1 1.0 C4 A:VIS1202 2.7 0.0 1.0 O2 A:VIS1202 3.0 0.4 1.0 NH1 A:ARG400 3.0 0.4 1.0 C7 A:VIS1202 3.1 0.7 1.0 NE2 A:GLN477 3.2 0.6 1.0 CD A:GLN477 3.8 0.1 1.0 CG A:GLN477 4.0 0.7 1.0 C1 A:VIS1202 4.0 0.5 1.0 C3 A:VIS1202 4.0 1.0 1.0 CZ A:ARG400 4.3 0.4 1.0 CB A:ASP473 4.3 0.8 1.0 N A:VIS1202 4.3 0.9 1.0 C2 A:VIS1202 4.5 0.8 1.0 CG A:ASP473 4.5 0.5 1.0 OE1 A:GLN477 4.7 0.6 1.0 CD1 A:TYR394 4.8 91.1 1.0 O A:TYR394 4.8 94.2 1.0 OD1 A:ASP473 4.8 0.1 1.0 NH2 A:ARG400 4.9 0.6 1.0 OD2 A:ASP473 5.0 0.7 1.0 CG A:PRO513 5.0 0.4 1.0

Chlorine binding site 3 out of 4 in the Structure of Human Smoothened in Complex with Vismodegib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Human Smoothened in Complex with Vismodegib within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1202 b:0.6 occ:1.00 CL1 B:VIS1202 0.0 0.6 1.0 C11 B:VIS1202 1.7 0.8 1.0 C10 B:VIS1202 2.7 1.0 1.0 C12 B:VIS1202 2.7 0.1 1.0 C14 B:VIS1202 3.1 0.2 1.0 C15 B:VIS1202 3.5 0.3 1.0 CD1 B:LEU522 3.6 0.2 1.0 N1 B:VIS1202 3.9 0.4 1.0 CB B:SER387 3.9 85.9 1.0 CH2 B:TRP281 4.0 87.7 1.0 C9 B:VIS1202 4.0 0.8 1.0 C13 B:VIS1202 4.0 0.6 1.0 CA B:SER387 4.1 84.6 1.0 CG B:LEU522 4.1 0.5 1.0 CZ3 B:TRP281 4.3 88.1 1.0 CD2 B:LEU522 4.3 0.8 1.0 CB B:GLU518 4.3 0.2 1.0 SD B:MET230 4.4 0.4 1.0 C16 B:VIS1202 4.5 0.8 1.0 C8 B:VIS1202 4.5 0.1 1.0 CE B:MET230 4.5 0.6 1.0 CD1 B:ILE234 4.6 0.6 1.0 O B:GLU518 4.6 0.3 1.0 C18 B:VIS1202 4.8 0.9 1.0 N B:SER387 4.8 86.4 1.0 CG B:MET230 4.9 0.6 1.0 OE2 B:GLU518 5.0 0.6 1.0

Chlorine binding site 4 out of 4 in the Structure of Human Smoothened in Complex with Vismodegib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Human Smoothened in Complex with Vismodegib within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1202 b:0.3 occ:1.00 CL B:VIS1202 0.0 0.3 1.0 C5 B:VIS1202 1.7 0.1 1.0 C6 B:VIS1202 2.7 0.2 1.0 C4 B:VIS1202 2.7 0.6 1.0 O2 B:VIS1202 3.0 0.4 1.0 NE2 B:GLN477 3.0 0.1 1.0 NH1 B:ARG400 3.0 0.5 1.0 C7 B:VIS1202 3.1 0.8 1.0 OD2 B:ASP473 3.4 0.3 1.0 CD B:GLN477 3.7 0.6 1.0 CB B:ASP473 3.8 0.1 1.0 CG B:ASP473 3.8 0.4 1.0 OE1 B:GLN477 3.9 0.9 1.0 C1 B:VIS1202 4.0 0.2 1.0 C3 B:VIS1202 4.0 0.1 1.0 CZ B:ARG400 4.3 0.1 1.0 N B:VIS1202 4.3 0.8 1.0 C2 B:VIS1202 4.5 0.3 1.0 CZ3 B:TRP480 4.6 0.1 1.0 CG B:PRO513 4.7 0.9 1.0 CE3 B:TRP480 4.7 0.1 1.0 CA B:ASP473 4.7 1.0 1.0 O B:ASP473 4.7 0.0 1.0 OD1 B:ASP473 4.7 0.2 1.0 CB B:PRO513 4.8 0.8 1.0 CG B:GLN477 4.9 0.9 1.0 C B:ASP473 4.9 0.3 1.0 NH2 B:ARG400 4.9 0.0 1.0

E.F.Byrne, R.Sircar, P.S.Miller, G.Hedger, G.Luchetti, S.Nachtergaele, M.D.Tully, L.Mydock-Mcgrane, D.F.Covey, R.P.Rambo, M.S.Sansom, S.Newstead, R.Rohatgi, C.Siebold. Structural Basis of Smoothened Regulation By Its Extracellular Domains. Nature V. 535 517 2016.
ISSN: ESSN 1476-4687
PubMed: 27437577
DOI: 10.1038/NATURE18934