Research workbench
Structure of VEGFR2 kinase domain in complex with BIBF1120
Analyse Structure of VEGFR2 kinase domain in complex with BIBF1120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C7Q
- Type
- protein
- Length
- 291 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor receptor 2
- EC
- 2.7.10.1
- UniProt
- P35968
- Ligands
- XIN, SO4
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 291 | 42% helix, 16% strand | P35968 |
Ligands and binding sites
- XIN · Methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl) acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.74 | 0.79 | 63 | SO4, XIN |
| 2 | 102 | 0.34 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 5 modified (artifact, phosphorylation).
Compared structures
- 3C7Q · Structure of VEGFR2 kinase domain in complex with BIBF1120 · the same entry in another collection · chain A against A, TM-score 1.00
- P35968 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 2… · 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 P35968
- Elsewhere: RCSB PDB 3C7Q · PDBe 3C7Q · UniProt P35968
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