MolNFT v1 · #124358 · protein
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with an N-trifluoroethyl obhs-N derivative
5KCW · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with an N-trifluoroethyl obhs-N…”. X-ray diffraction, 1 ligand (OB9), 7 pockets (best druggability 0.85). MolNFT v1 #124358 on GenesisL1…
- PDB
- 5KCW
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; NCOA2
- UniProt
- P03372
- Ligands
- OB9
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 233 | 70% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 224 | 70% helix, 4% strand | P03372 |
| C | NCOA2 | protein | 10 | 70% helix, 0% strand | — |
| D | NCOA2 | protein | 9 | 67% helix, 0% strand | — |
Ligands and binding sites
- OB9 · (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-N-phenyl-N-(2,2,2-trifluoroethyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.85 | 0.94 | 38 | OB9 |
| 2 | 317 | 0.81 | 0.91 | 26 | OB9 |
| 3 | 92 | 0.67 | 0.91 | 20 | empty |
| 4 | 84 | 0.63 | 0.90 | 17 | empty |
| 5 | 99 | 0.46 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1670 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 512 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 508 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5KCW · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with an… · the same entry in another collection · chain A against A, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P03372
- Elsewhere: RCSB PDB 5KCW · PDBe 5KCW · UniProt P03372
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.