Research workbench
Crystal structure of comt in complex with [3-(2,4-dimethyl-1,3- thiazol-5-yl)-1H-pyrazol-5-yl]-(4-phenylpiperazin-1-YL)METHANONE
Analyse Crystal structure of comt in complex with [3-(2,4-dimethyl-1,3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LR6
- Type
- protein
- Length
- 852 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
- 731, CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 212 | 45% helix, 23% strand | P22734 |
| B | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 212 | 46% helix, 25% strand | P22734 |
| C | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 214 | 45% helix, 24% strand | P22734 |
| D | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 214 | 44% helix, 24% strand | P22734 |
Ligands and binding sites
- 731 · [5-(2,4-dimethyl-1,3-thiazol-5-yl)-1~{H}-pyrazol-3-yl]-(4-phenylpiperazin-1-yl)methanone · ligand · 4 copies · chains A, C, B, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.81 | 0.82 | 100 | 731, NHE |
| 2 | 52 | 0.66 | 0.95 | 22 | empty |
| 3 | 418 | 0.66 | 0.79 | 44 | 731 |
| 4 | 145 | 0.57 | 0.82 | 30 | empty |
| 5 | 209 | 0.52 | 0.77 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–C · 612 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 508 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 477 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 147 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LR6 · Crystal Structure of COMT in complex with [3-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-5… · 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 A 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 5LR6 · PDBe 5LR6 · UniProt P22734
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