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Crystal structure of human VEGFR2 kinase domain with a novel pyrrolopyrimidine inhibitor.

Analyse Crystal structure of human VEGFR2 kinase domain with a novel pyrrolopyrimidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VHE
Type: protein
Length: 303 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: 42Q
Pockets: 2 · best druggability 0.75

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 2 (EC 2.7.10.1)	protein	303	41% helix, 17% strand	P35968

Ligands and binding sites

42Q · 1-{2-fluoro-4-[(5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy]phenyl}-3-[3-(trifluoromethyl)phenyl]urea · ligand · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	571	0.75	0.82	66	42Q
2	50	0.23	0.71	18	empty

Compared structures

3VHE · Crystal structure of human VEGFR2 kinase domain with a novel pyrrolopyrimidine 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 3VHE · PDBe 3VHE · UniProt P35968

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