MolNFT v1 · #150311 · protein
Crystal structure of CCR2A in complex with mk-0812
6GPS · C-C chemokine receptor type 2,RUBREDOXIN,C-C chemokine…: “Crystal structure of CCR2A in complex with mk-0812”. X-ray diffraction, 2 ligands (F7N, ZN), 6 pockets (best druggability 0.73). MolNFT v1 #150311 on GenesisL1: 3D structure…
- PDB
- 6GPS
- Type
- protein
- Length
- 330 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-C chemokine receptor type 2,RUBREDOXIN,C-C chemokine receptor type 2
- UniProt
- P41597, P00268
- Ligands
- F7N, ZN
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-C chemokine receptor type 2,RUBREDOXIN,C-C chemokine receptor type 2 | protein | 330 | 68% helix, 7% strand | P41597, P00268 |
Ligands and binding sites
- F7N · [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.73 | 0.79 | 47 | F7N |
| 2 | 82 | 0.49 | 0.83 | 19 | empty |
| 3 | 77 | 0.45 | 0.81 | 14 | empty |
| 4 | 116 | 0.40 | 0.75 | 18 | empty |
| 5 | 64 | 0.37 | 0.79 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6GPS · Crystal structure of CCR2A in complex with mk-0812 · the same entry in another collection · chain A against A, TM-score 1.00
- P41597 · AlphaFold monomer V2.0 prediction for C-C chemokine receptor type 2 (P41597) · a predicted model of the same protein · chain A against A, TM-score 0.81
- P00268 · AlphaFold monomer V2.0 prediction for rubredoxin (P00268) · a predicted model of the same protein · chain A against A, TM-score 0.16
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 P41597
- Every structure of UniProt P00268
- Elsewhere: RCSB PDB 6GPS · PDBe 6GPS · UniProt P41597 · UniProt P00268
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