MolNFT v1 · #179863 · protein
Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with covalent compound 19
7KIA · Fibroblast growth factor receptor 2: “Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with covalent compound 19”. X-ray diffraction, 2 ligands (WFD, NA), 7 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 7KIA
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibroblast growth factor receptor 2
- EC
- 2.7.10.1
- UniProt
- P21802
- Ligands
- WFD, NA
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 287 | 38% helix, 18% strand | P21802 |
| B | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 288 | 39% helix, 18% strand | P21802 |
Ligands and binding sites
- WFD · 1-[4-(4-{4-(4-methylpiperazin-1-yl)-6-[(3-methyl-1H-pyrazol-5-yl)amino]pyrimidin-2-yl}phenyl)piperidin-1-yl]prop-2-en-1-one · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- FLC · Citrate anion · additive · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.83 | 0.84 | 91 | WFD, FLC |
| 2 | 147 | 0.48 | 0.77 | 23 | empty |
| 3 | 139 | 0.43 | 0.76 | 26 | empty |
| 4 | 53 | 0.37 | 0.80 | 14 | FLC |
| 5 | 76 | 0.37 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1168 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7KIA · Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with covalent… · the same entry in another collection · chain A against A, TM-score 1.00
- P21802 · AlphaFold monomer V2.0 prediction for fibroblast growth factor receptor 2 (P21802) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P21802
- Elsewhere: RCSB PDB 7KIA · PDBe 7KIA · UniProt P21802
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