Crystal structure of human C5A receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist NDT9513727

Structure

x-ray diffraction · 2 distinct chains · 80% helix, 4% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · chains B, L
• 9P2 · 1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-diphenyl-imidazol-4-yl) methyl]methanamine · ligand · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• B–L · 765 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified, 1 covalent, 1 disulfide (nonstandard, covalent ligand, disulfide, alkylation).

Compared structures

• 6C1Q · Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53… · the same entry in another collection · chain B against B, TM-score 1.00
• P21730 · AlphaFold monomer V2.0 prediction for C5A anaphylatoxin chemotactic receptor 1 (P21730) · a predicted model of the same protein · chain B against A, TM-score 0.77
• P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.24

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P0ABE7
• Every structure of UniProt P21730
• Elsewhere: RCSB PDB 6C1Q · PDBe 6C1Q · UniProt P0ABE7 · UniProt P21730