Research workbench
Crystal structure of VEGFR1 in complex with N-(4-chlorophenyl)-2- ((pyridin-4-YLMETHYL)AMINO)BENZAMIDE
Analyse Crystal structure of VEGFR1 in complex with N-(4-chlorophenyl)-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HNG
- Type
- protein
- Length
- 288 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor receptor 1
- EC
- 2.7.10.1
- UniProt
- P17948
- Ligands
- 8ST, CL
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor receptor 1 (EC 2.7.10.1) | protein | 288 | 41% helix, 17% strand | P17948 |
Ligands and binding sites
- 8ST · N-(4-chlorophenyl)-2-[(pyridin-4-ylmethyl)amino]benzamide · ligand · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.74 | 0.82 | 56 | 8ST |
Compared structures
- 3HNG · Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amin… · the same entry in another collection · chain A against A, TM-score 1.00
- P17948 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 1… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P17948
- Elsewhere: RCSB PDB 3HNG · PDBe 3HNG · UniProt P17948
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