MolNFT v1 · #120050 · protein
Crystal structure of EGFR 696-988 T790M in complex with lxx-6-34
5GNK · Epidermal growth factor receptor: “Crystal structure of EGFR 696-988 T790M in complex with lxx-6-34”. X-ray diffraction, 3 ligands (80U, NO3, CL), 4 pockets (best druggability 0.69). MolNFT v1 #120050 on GenesisL1: 3D structure…
- PDB
- 5GNK
- Type
- protein
- Length
- 277 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- 80U, NO3, CL
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 277 | 42% helix, 18% strand | P00533 |
Ligands and binding sites
- 80U · 1-[(3R)-3-[4-azanyl-3-[3-chloranyl-4-[(1-methylimidazol-2-yl)methoxy]phenyl]pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]prop-2-en-1-one · ligand · chains A
- NO3 · Nitrate ion · ion · 11 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 19 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.69 | 0.84 | 32 | 80U, NO3, EDO |
| 2 | 71 | 0.38 | 0.78 | 16 | EDO |
| 3 | 51 | 0.32 | 0.77 | 12 | empty |
| 4 | 50 | 0.25 | 0.73 | 14 | EDO |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5GNK · Crystal structure of EGFR 696-988 T790M in complex with LXX-6-34 · the same entry in another collection · chain A against A, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P00533
- Elsewhere: RCSB PDB 5GNK · PDBe 5GNK · UniProt P00533
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