MolNFT v1 · #164584 · protein
FURANO[2,3-D]PRYMIDINE amides as notum inhibitors
6T2H · Palmitoleoyl-protein carboxylesterase notum: “FURANO[2,3-D]PRYMIDINE amides as notum inhibitors”. X-ray diffraction, 3 ligands (M9N, NAG, SO4), 3 pockets (best druggability 0.73). MolNFT v1 #164584 on GenesisL1: 3D structure…
- PDB
- 6T2H
- Type
- protein
- Length
- 354 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Palmitoleoyl-protein carboxylesterase notum
- EC
- 3.1.1.98
- UniProt
- Q6P988
- Ligands
- M9N, NAG, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Palmitoleoyl-protein carboxylesterase notum (EC 3.1.1.98) | protein | 354 | 33% helix, 18% strand | Q6P988 |
Ligands and binding sites
- M9N · 2-[[(4~{S})-5-chloranyl-6-methyl-1,2,3,4-tetrahydrothieno[2,3-d]pyrimidin-4-yl]sulfanyl]ethanoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
- EDO · 1,2-ethanediol · additive · 13 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.73 | 0.94 | 19 | M9N |
| 2 | 148 | 0.47 | 0.77 | 21 | empty |
| 3 | 82 | 0.37 | 0.77 | 16 | SO4 |
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6T2H · Furano[2,3-d]prymidine amides as Notum inhibitors · the same entry in another collection · chain A against A, 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 Q6P988
- Elsewhere: RCSB PDB 6T2H · PDBe 6T2H · UniProt Q6P988
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