MolNFT v1 · #28300 · protein
Crystal structure of human liver carboxylesterase 1 in complex with tamoxifen
1YA4 · CES1 protein: “Crystal structure of human liver carboxylesterase 1 in complex with tamoxifen”. X-ray diffraction, 4 ligands (CTX, NAG, SIA), 17 pockets (best druggability 0.81). MolNFT v1 #28300 on GenesisL1: 3D structure, binding…
- PDB
- 1YA4
- Type
- protein
- Length
- 1,595 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CES1 protein
- EC
- 3.1.1.1
- UniProt
- P23141
- Ligands
- CTX, NAG, SIA, SO4
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CES1 protein (EC 3.1.1.1) | protein | 531 | 36% helix, 16% strand | P23141 |
| B, C | CES1 protein (EC 3.1.1.1) | protein | 532 | 36% helix, 16% strand | P23141 |
Ligands and binding sites
- CTX · (Z)-2-[4-(1,2)-diphenyl-1-butenyl)-phenoxy]-N,N-dimethylethanamine · ligand · 6 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.81 | 0.82 | 127 | SO4, SIA |
| 2 | 316 | 0.80 | 0.90 | 41 | CTX |
| 3 | 301 | 0.80 | 0.90 | 40 | CTX |
| 4 | 270 | 0.80 | 0.91 | 37 | CTX |
| 5 | 371 | 0.64 | 0.79 | 48 | SIA |
Interfaces
3 interfaces between chains.
- B–C · 601 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 593 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 592 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1YA4 · Crystal Structure of Human Liver Carboxylesterase 1 in complex with tamoxifen · the same entry in another collection · chain C against C, TM-score 1.00
- P23141 · AlphaFold monomer V2.0 prediction for liver carboxylesterase 1 (P23141) · a predicted model of the same protein · chain B 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 1YA4 · PDBe 1YA4 · UniProt P23141
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