MolNFT v1 · #130288 · protein
Crystal structure of comt in complex with [5-(2,4-dimethyl-1,3- thiazol-5-yl)-1H-pyrazol-3-YL]METHANAMINE
5P8W · Catechol O-methyltransferase: “Crystal structure of comt in complex with [5-(2,4-dimethyl-1,3- thiazol-5-yl)-1H-pyrazol-3-YL]METHANAMINE”. X-ray diffraction, 2 ligands (O01, NA), 5 pockets (best druggability 0.84). MolNFT v1 #130288…
- PDB
- 5P8W
- Type
- protein
- Length
- 640 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol O-methyltransferase
- EC
- 2.1.1.6
- UniProt
- P22734
- Ligands
- O01, NA
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 215 | 48% helix, 26% strand | P22734 |
| B | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 213 | 48% helix, 26% strand | P22734 |
| C | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 212 | 46% helix, 23% strand | P22734 |
Ligands and binding sites
- O01 · [5-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-3-yl]methanamine · ligand · 3 copies · chains A, C, B
- NA · Sodium ion · metal · 5 copies · chains A, B, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains A, B, C
- FMT · Formic acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.84 | 0.88 | 65 | DTT, O01 |
| 2 | 617 | 0.83 | 0.87 | 75 | DTT, O01 |
| 3 | 617 | 0.78 | 0.84 | 54 | DTT, O01 |
| 4 | 175 | 0.55 | 0.80 | 29 | NA |
| 5 | 113 | 0.41 | 0.76 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2652 Ų buried · 78 hydrogen bonds · protein-protein
- B–C · 770 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 611 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (additive adduct).
Compared structures
- 5P8W · Crystal Structure of COMT in complex with [5-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-3… · 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 C against A, TM-score 0.95
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 5P8W · PDBe 5P8W · UniProt P22734
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