MolNFT v1 · #123943 · protein
Crystal structure of comt in complex with a thiazole ligand
5K09 · Catechol O-methyltransferase: “Crystal structure of comt in complex with a thiazole ligand”. X-ray diffraction, 3 ligands (6PQ, K, PO4), 20 pockets (best druggability 0.84). MolNFT v1 #123943 on GenesisL1: 3D structure, binding…
- PDB
- 5K09
- Type
- protein
- Length
- 5,174 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol O-methyltransferase
- EC
- 2.1.1.6
- UniProt
- P22734
- Ligands
- 6PQ, K, PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, R | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 217 | 47% helix, 24% strand | P22734 |
| B, D, E, I, K, M, P, S, T, U, V, W, X | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 215 | 47% helix, 21% strand | P22734 |
| C, F, H, J, L, N, O, Q | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 216 | 46% helix, 21% strand | P22734 |
Ligands and binding sites
- 6PQ · 5-{3-[(4-methoxyphenyl)methyl]-1H-pyrazol-5-yl}-2,4-dimethyl-1,3-thiazole · ligand · 24 copies · chains A, C, D, B, H, Q, G, W, E, F, I, T, K, R, X, J, M, O, N, L, V, U, P, S
- K · Potassium ion · metal · 58 copies · chains A, D, B, Q, C, G, E, W, F, I, H, R, J, O, K, N, L, M, P, X, S, T, U, V
- PO4 · Phosphate ion · ion · 12 copies · chains C, D, H, I, K, M, N, Q, S, T, V, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.84 | 0.87 | 105 | 6PQ |
| 2 | 638 | 0.82 | 0.87 | 100 | 6PQ |
| 3 | 317 | 0.82 | 0.93 | 56 | 6PQ |
| 4 | 318 | 0.82 | 0.92 | 53 | 6PQ |
| 5 | 506 | 0.82 | 0.88 | 77 | 6PQ |
Interfaces
55 interfaces between chains.
- B–Q · 1216 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1210 Ų buried · 22 hydrogen bonds · protein-protein
- U–V · 1208 Ų buried · 23 hydrogen bonds · protein-protein
- J–O · 1200 Ų buried · 21 hydrogen bonds · protein-protein
- S–T · 1200 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5K09 · Crystal Structure of COMT in complex with a thiazole ligand · the same entry in another collection · chain K against K, TM-score 1.00
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 P22734
- Elsewhere: RCSB PDB 5K09 · PDBe 5K09 · UniProt P22734
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