Chlorine in PDB 8gfa: Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791

The structure of Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791 (pdb code 8gfa). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791, PDB code: 8gfa:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1202 b:6.1 occ:1.00 CL17 A:ZEI1202 0.0 6.1 1.0 C16 A:ZEI1202 1.7 6.1 1.0 HD1 A:PHE543 2.6 34.4 1.0 C15 A:ZEI1202 2.7 6.1 1.0 C18 A:ZEI1202 2.7 6.1 1.0 H10 A:ZEI1202 2.8 6.1 1.0 H3 A:ZEI1202 2.8 6.1 1.0 HE1 B:PHE591 3.3 20.5 1.0 H212 B:POV1201 3.3 18.1 1.0 HD12 B:LEU663 3.3 24.1 1.0 CD1 A:PHE543 3.4 34.4 1.0 H21B B:POV1201 3.5 18.1 1.0 HE1 A:PHE543 3.5 34.4 1.0 HB3 A:ALA546 3.8 31.0 1.0 CE1 A:PHE543 3.9 34.4 1.0 HB3 B:ALA666 3.9 21.2 1.0 C212 B:POV1201 3.9 18.1 1.0 HB1 B:ALA666 3.9 21.2 1.0 C19 A:ZEI1202 4.0 6.1 1.0 C14 A:ZEI1202 4.0 6.1 1.0 H214 B:POV1201 4.0 18.1 1.0 HB1 A:ALA546 4.0 31.0 1.0 HD13 B:LEU663 4.1 24.1 1.0 CE1 B:PHE591 4.1 20.5 1.0 HA B:LEU663 4.1 24.1 1.0 CD1 B:LEU663 4.1 24.1 1.0 HA A:PHE543 4.1 34.4 1.0 HB2 B:ALA666 4.1 21.2 1.0 CB B:ALA666 4.2 21.2 1.0 HG A:LEU547 4.3 32.5 1.0 HZ B:PHE591 4.3 20.5 1.0 HD11 B:LEU663 4.3 24.1 1.0 CB A:ALA546 4.4 31.0 1.0 H21D B:POV1201 4.4 18.1 1.0 C13 A:ZEI1202 4.5 6.1 1.0 HG22 B:ILE662 4.5 26.2 1.0 C214 B:POV1201 4.5 18.1 1.0 HB3 A:PHE543 4.6 34.4 1.0 CG A:PHE543 4.6 34.4 1.0 CZ B:PHE591 4.6 20.5 1.0 C213 B:POV1201 4.6 18.1 1.0 H21C B:POV1201 4.6 18.1 1.0 H4 A:ZEI1202 4.7 6.1 1.0 H9 A:ZEI1202 4.7 6.1 1.0 HB2 A:ALA546 4.9 31.0 1.0 CB A:PHE543 4.9 34.4 1.0 CA A:PHE543 4.9 34.4 1.0 H21D A:POV1201 5.0 18.4 1.0 CA B:LEU663 5.0 24.1 1.0

Chlorine binding site 2 out of 4 in the Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1204 b:4.2 occ:1.00 CL17 B:ZEI1204 0.0 4.2 1.0 C16 B:ZEI1204 1.7 4.2 1.0 HD1 B:PHE543 2.6 34.1 1.0 C15 B:ZEI1204 2.7 4.2 1.0 C18 B:ZEI1204 2.7 4.2 1.0 H10 B:ZEI1204 2.8 4.2 1.0 H3 B:ZEI1204 2.8 4.2 1.0 HE1 C:PHE591 3.3 20.7 1.0 HD12 C:LEU663 3.3 24.4 1.0 H212 B:POV1202 3.3 17.9 1.0 CD1 B:PHE543 3.5 34.1 1.0 H21B B:POV1202 3.5 17.9 1.0 HE1 B:PHE543 3.5 34.1 1.0 HB3 B:ALA546 3.9 30.8 1.0 C212 B:POV1202 3.9 17.9 1.0 CE1 B:PHE543 3.9 34.1 1.0 H214 B:POV1202 3.9 17.9 1.0 HB3 C:ALA666 4.0 21.3 1.0 C19 B:ZEI1204 4.0 4.2 1.0 C14 B:ZEI1204 4.0 4.2 1.0 HB1 C:ALA666 4.0 21.3 1.0 HD13 C:LEU663 4.0 24.4 1.0 CD1 C:LEU663 4.0 24.4 1.0 CE1 C:PHE591 4.1 20.7 1.0 HB1 B:ALA546 4.1 30.8 1.0 HA C:LEU663 4.1 24.4 1.0 HA B:PHE543 4.2 34.1 1.0 HB2 C:ALA666 4.2 21.3 1.0 CB C:ALA666 4.2 21.3 1.0 HD11 C:LEU663 4.3 24.4 1.0 HZ C:PHE591 4.3 20.7 1.0 HG B:LEU547 4.3 32.3 1.0 H21D B:POV1202 4.4 17.9 1.0 CB B:ALA546 4.4 30.8 1.0 C13 B:ZEI1204 4.5 4.2 1.0 C214 B:POV1202 4.5 17.9 1.0 HG22 C:ILE662 4.6 26.5 1.0 HB3 B:PHE543 4.6 34.1 1.0 CZ C:PHE591 4.6 20.7 1.0 C213 B:POV1202 4.6 17.9 1.0 H21C B:POV1202 4.6 17.9 1.0 CG B:PHE543 4.6 34.1 1.0 H4 B:ZEI1204 4.7 4.2 1.0 H9 B:ZEI1204 4.7 4.2 1.0 HB2 B:ALA546 4.9 30.8 1.0 CB B:PHE543 4.9 34.1 1.0 CA B:PHE543 4.9 34.1 1.0 H21D B:POV1203 5.0 17.9 1.0 CD1 C:PHE591 5.0 20.7 1.0 HD1 C:PHE591 5.0 20.7 1.0

Chlorine binding site 3 out of 4 in the Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1202 b:5.8 occ:1.00 CL17 C:ZEI1202 0.0 5.8 1.0 C16 C:ZEI1202 1.7 5.8 1.0 HD1 C:PHE543 2.6 34.5 1.0 C15 C:ZEI1202 2.7 5.8 1.0 C18 C:ZEI1202 2.7 5.8 1.0 H10 C:ZEI1202 2.8 5.8 1.0 H3 C:ZEI1202 2.8 5.8 1.0 HE1 D:PHE591 3.3 20.6 1.0 H212 D:POV1201 3.3 17.6 1.0 HD12 D:LEU663 3.3 24.4 1.0 CD1 C:PHE543 3.5 34.5 1.0 H21B D:POV1201 3.5 17.6 1.0 HE1 C:PHE543 3.5 34.5 1.0 HB3 C:ALA546 3.9 31.0 1.0 C212 D:POV1201 3.9 17.6 1.0 CE1 C:PHE543 3.9 34.5 1.0 HB3 D:ALA666 3.9 21.3 1.0 HB1 D:ALA666 3.9 21.3 1.0 H214 D:POV1201 3.9 17.6 1.0 C19 C:ZEI1202 4.0 5.8 1.0 C14 C:ZEI1202 4.0 5.8 1.0 HD13 D:LEU663 4.0 24.4 1.0 HB1 C:ALA546 4.1 31.0 1.0 CD1 D:LEU663 4.1 24.4 1.0 HA D:LEU663 4.1 24.4 1.0 CE1 D:PHE591 4.1 20.6 1.0 HA C:PHE543 4.1 34.5 1.0 HB2 D:ALA666 4.1 21.3 1.0 CB D:ALA666 4.2 21.3 1.0 HG C:LEU547 4.3 32.6 1.0 HZ D:PHE591 4.3 20.6 1.0 HD11 D:LEU663 4.3 24.4 1.0 H21D D:POV1201 4.4 17.6 1.0 CB C:ALA546 4.4 31.0 1.0 C13 C:ZEI1202 4.5 5.8 1.0 C214 D:POV1201 4.5 17.6 1.0 HG22 D:ILE662 4.5 26.5 1.0 HB3 C:PHE543 4.6 34.5 1.0 CG C:PHE543 4.6 34.5 1.0 C213 D:POV1201 4.6 17.6 1.0 CZ D:PHE591 4.6 20.6 1.0 H21C D:POV1201 4.6 17.6 1.0 H4 C:ZEI1202 4.7 5.8 1.0 H9 C:ZEI1202 4.7 5.8 1.0 HB2 C:ALA546 4.9 31.0 1.0 CB C:PHE543 4.9 34.5 1.0 CA C:PHE543 4.9 34.5 1.0 H21D C:POV1201 5.0 17.6 1.0

Chlorine binding site 4 out of 4 in the Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1203 b:6.0 occ:1.00 CL17 D:ZEI1203 0.0 6.0 1.0 C16 D:ZEI1203 1.7 6.0 1.0 HD1 D:PHE543 2.6 34.6 1.0 C18 D:ZEI1203 2.7 6.0 1.0 C15 D:ZEI1203 2.7 6.0 1.0 H10 D:ZEI1203 2.8 6.0 1.0 H3 D:ZEI1203 2.8 6.0 1.0 HE1 A:PHE591 3.2 20.8 1.0 HD12 A:LEU663 3.2 24.4 1.0 H212 A:POV1211 3.3 19.0 1.0 CD1 D:PHE543 3.5 34.6 1.0 H21B A:POV1211 3.5 19.0 1.0 HE1 D:PHE543 3.5 34.6 1.0 HB3 A:ALA666 3.9 21.5 1.0 HB3 D:ALA546 3.9 31.1 1.0 C212 A:POV1211 3.9 19.0 1.0 HB1 A:ALA666 3.9 21.5 1.0 CE1 D:PHE543 3.9 34.6 1.0 H214 A:POV1211 3.9 19.0 1.0 HD13 A:LEU663 4.0 24.4 1.0 CD1 A:LEU663 4.0 24.4 1.0 C19 D:ZEI1203 4.0 6.0 1.0 C14 D:ZEI1203 4.0 6.0 1.0 HA A:LEU663 4.0 24.4 1.0 CE1 A:PHE591 4.0 20.8 1.0 HB1 D:ALA546 4.1 31.1 1.0 HB2 A:ALA666 4.1 21.5 1.0 CB A:ALA666 4.1 21.5 1.0 HA D:PHE543 4.2 34.6 1.0 HD11 A:LEU663 4.2 24.4 1.0 HZ A:PHE591 4.3 20.8 1.0 HG D:LEU547 4.3 32.6 1.0 H21D A:POV1211 4.4 19.0 1.0 CB D:ALA546 4.4 31.1 1.0 HG22 A:ILE662 4.5 26.4 1.0 C13 D:ZEI1203 4.5 6.0 1.0 C214 A:POV1211 4.5 19.0 1.0 CZ A:PHE591 4.6 20.8 1.0 HB3 D:PHE543 4.6 34.6 1.0 C213 A:POV1211 4.6 19.0 1.0 H21C A:POV1211 4.6 19.0 1.0 CG D:PHE543 4.6 34.6 1.0 H4 D:ZEI1203 4.7 6.0 1.0 H9 D:ZEI1203 4.7 6.0 1.0 HB2 D:ALA546 4.9 31.1 1.0 CA A:LEU663 4.9 24.4 1.0 CB D:PHE543 4.9 34.6 1.0 HD1 A:PHE591 4.9 20.8 1.0 CD1 A:PHE591 4.9 20.8 1.0 CA D:PHE543 4.9 34.6 1.0 H21D D:POV1202 4.9 19.3 1.0

A.Neuberger, M.Oda, Y.A.Nikolaev, K.D.Nadezhdin, E.O.Gracheva, S.N.Bagriantsev, A.I.Sobolevsky. Human TRPV1 Structure and Inhibition By the Analgesic Sb-366791. Nat Commun V. 14 2451 2023.
ISSN: ESSN 2041-1723
PubMed: 37117175
DOI: 10.1038/S41467-023-38162-9