MolNFT v1 · #54487 · protein
X-ray structure of human butyrylcholinesterase inhibited by racemic vr
2XQG: “X-ray structure of human butyrylcholinesterase inhibited by racemic vr”. X-ray diffraction, 10 ligands (VR, GLY, NAG), 5 pockets (best druggability 0.79). MolNFT v1 #54487 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2XQG
- Type
- protein
- Length
- 527 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholinesterase
- EC
- 3.1.1.8
- UniProt
- P06276
- Ligands
- VR, GLY, NAG, FUL, CA, NA, UNX, SO4, BR, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholinesterase (EC 3.1.1.8) | protein | 527 | 38% helix, 17% strand | P06276 |
Ligands and binding sites
- VR · 2-methylpropyl hydrogen (R)-methylphosphonate · ligand · chains A
- GLY · Glycine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- UNX · Unknown atom or ion · ion · 23 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- BR · Bromide ion · ion · chains A
- CL · Chloride ion · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.79 | 0.84 | 47 | UNX, VR, CA |
| 2 | 575 | 0.69 | 0.78 | 47 | UNX |
| 3 | 129 | 0.43 | 0.77 | 31 | CA |
| 4 | 61 | 0.41 | 0.81 | 14 | empty |
| 5 | 72 | 0.35 | 0.76 | 19 | CA |
Modifications
Observed in the structure: 6 glycan, 3 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
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 P06276
- Elsewhere: RCSB PDB 2XQG · PDBe 2XQG · UniProt P06276
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