Research workbench
Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with covalent compound 19
Analyse Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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