MolNFT v1 · #126224 · protein
Crystal structure of the human cc chemokine receptor type 9 (CCR9) in complex with vercirnon
5LWE · C-C chemokine receptor type 9: “Crystal structure of the human cc chemokine receptor type 9 (CCR9) in complex with vercirnon”. X-ray diffraction, 3 ligands (OLA, 79K, CLR), 11 pockets (best druggability 0.79). MolNFT v1 #126224 on…
- PDB
- 5LWE
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-C chemokine receptor type 9
- UniProt
- P51686
- Ligands
- OLA, 79K, CLR
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-C chemokine receptor type 9 | protein | 275 | 88% helix, 0% strand | P51686 |
| B | C-C chemokine receptor type 9 | protein | 285 | 87% helix, 0% strand | P51686 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 28 copies · chains A, B
- 79K · Vercirnon · ligand · 2 copies · chains A, B
- CLR · Cholesterol · ligand · chains A
- MLI · Malonate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.79 | 0.93 | 29 | 79K |
| 2 | 298 | 0.72 | 0.85 | 43 | 79K, MLI |
| 3 | 582 | 0.69 | 0.77 | 63 | empty |
| 4 | 237 | 0.51 | 0.75 | 25 | empty |
| 5 | 55 | 0.45 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 517 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5LWE · Crystal structure of the human CC chemokine receptor type 9 (CCR9) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P51686 · AlphaFold monomer V2.0 prediction for C-C chemokine receptor type 9 (P51686) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P51686
- Elsewhere: RCSB PDB 5LWE · PDBe 5LWE · UniProt P51686
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