Research workbench
Crystal structure of comt in complex with 5-[5-[1-(4-methoxyphenyl) cyclopropyl]-1H-pyrazol-3-yl]-2,4-dimethyl-1,3-thiazole
Analyse Crystal structure of comt in complex with 5-[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
- 5K0L
- Type
- protein
- Length
- 875 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol O-methyltransferase
- EC
- 2.1.1.6
- UniProt
- P22734
- Ligands
- 6P2, MG, K
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 219 | 45% helix, 23% strand | P22734 |
| B | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 218 | 45% helix, 23% strand | P22734 |
Ligands and binding sites
- 6P2 · 5-{3-[1-(4-methoxyphenyl)cyclopropyl]-1H-pyrazol-5-yl}-2,4-dimethyl-1,3-thiazole · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.85 | 0.86 | 103 | 6P2, NHE |
| 2 | 538 | 0.74 | 0.82 | 66 | empty |
| 3 | 193 | 0.62 | 0.83 | 40 | 6P2, NHE |
| 4 | 80 | 0.52 | 0.85 | 21 | 6P2 |
| 5 | 66 | 0.30 | 0.74 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–C · 666 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 544 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 523 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 192 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5K0L · Crystal Structure of COMT in complex with 5-[5-[1-(4-methoxyphenyl)cyclopropyl]-1H-pyrazol… · the same entry in another collection · chain D against D, TM-score 1.00
- P22734 · AlphaFold monomer V2.0 prediction for catechol O-methyltransferase (P22734) · a predicted model of the same protein · chain D 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 5K0L · PDBe 5K0L · UniProt P22734
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