MolNFT v1 · #15195 · protein
Crystal structure of human liver carboxylesterase in complexed with homatropine, a cocaine analogue
1MX5: “Crystal structure of human liver carboxylesterase in complexed with homatropine, a cocaine analogue”. X-ray diffraction, 4 ligands (HTQ, NAG, SIA), 20 pockets (best druggability 0.80). MolNFT v1 #15195 on GenesisL1: 3D structure…
- PDB
- 1MX5
- Type
- protein
- Length
- 3,188 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Liver carboxylesterase I
- EC
- 3.1.1.1
- UniProt
- P23141
- Ligands
- HTQ, NAG, SIA, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Liver carboxylesterase I (EC 3.1.1.1) | protein | 532 | 36% helix, 16% strand | P23141 |
| B, C, E, F | Liver carboxylesterase I (EC 3.1.1.1) | protein | 531 | 37% helix, 16% strand | P23141 |
Ligands and binding sites
- HTQ · Homotropine · ligand · 12 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D, E, F
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C, D, F
- CL · Chloride ion · ion · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.80 | 0.91 | 40 | CL, HTQ |
| 2 | 239 | 0.79 | 0.92 | 39 | CL, HTQ |
| 3 | 848 | 0.79 | 0.82 | 120 | SIA |
| 4 | 260 | 0.79 | 0.91 | 38 | HTQ |
| 5 | 227 | 0.78 | 0.91 | 37 | HTQ |
Interfaces
7 interfaces between chains.
- B–C · 576 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 563 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 557 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 552 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 542 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 1MX5 · Crystal Structure of Human Liver Carboxylesterase in complexed with homatropine, a… · the same entry in another collection · chain F against F, TM-score 1.00
- P23141 · AlphaFold monomer V2.0 prediction for liver carboxylesterase 1 (P23141) · a predicted model of the same protein · chain F 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 P23141
- Elsewhere: RCSB PDB 1MX5 · PDBe 1MX5 · UniProt P23141
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