MolNFT v1 · #170070 · protein

Crystal structure of the kdr (VEGFR2) kinase domain in complex with a type-II inhibitor

6XVJ · Vascular endothelial growth factor receptor 2: “Crystal structure of the kdr (VEGFR2) kinase domain in complex with a type-II inhibitor”. X-ray diffraction, 1 ligand (O35), 3 pockets (best druggability 0.76). MolNFT v1 #170070 on…

PDB: 6XVJ
Type: protein
Length: 305 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: O35
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vascular endothelial growth factor receptor 2 (EC 2.7.10.1)	protein	305	42% helix, 18% strand	P35968

Ligands and binding sites

O35 · ~{N}-[3-[(dimethylamino)methyl]-5-methyl-phenyl]-2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanamide · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	614	0.76	0.82	55	O35
2	54	0.30	0.76	17	empty
3	64	0.26	0.72	19	empty

Compared structures

6XVJ · Crystal structure of the KDR (VEGFR2) kinase domain in complex with a type-II inhibitor · the same entry in another collection · chain A against A, TM-score 1.00

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 6XVJ · PDBe 6XVJ · UniProt P35968

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