Research workbench
Crystal structure of comt in complex with 4-[5-[1-(4-methoxyphenyl) ethyl]-1H-pyrazol-3-yl]-1,3-dimethylpyrazole
Analyse Crystal structure of comt in complex with 4-[5-[1-(4-methoxyphenyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K0G
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol O-methyltransferase
- EC
- 2.1.1.6
- UniProt
- P22734
- Ligands
- 6PM, NA
- Pockets
- 1 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 219 | 47% helix, 23% strand | P22734 |
| B | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 220 | 47% helix, 22% strand | P22734 |
Ligands and binding sites
- 6PM · 5-[(1S)-1-(4-methoxyphenyl)ethyl]-1',3'-dimethyl-1'H,2H-3,4'-bipyrazole · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.85 | 0.86 | 108 | NHE, 6PM, NA |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5K0G · Crystal Structure of COMT in complex with 4-[5-[1-(4-methoxyphenyl)ethyl]-1H-pyrazol-3-yl]… · the same entry in another collection · chain A against A, TM-score 1.00
- P22734 · AlphaFold monomer V2.0 prediction for catechol O-methyltransferase (P22734) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 5K0G · PDBe 5K0G · UniProt P22734
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