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Kdr in complex with ligand sorafenib

Analyse Kdr in complex with ligand sorafenib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WZE
Type: protein
Length: 298 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: BAX
Pockets: 1 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vascular endothelial growth factor receptor 2 (EC 2.7.10.1)	protein	298	40% helix, 17% strand	P35968

Ligands and binding sites

BAX · 4-{4-[({[4-chloro-3-(trifluoromethyl)phenyl]amino}carbonyl)amino]phenoxy}-N-methylpyridine-2-carboxamide · ligand · chains A
ACT · Acetate ion · additive · chains A
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	687	0.74	0.80	75	BAX

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

3WZE · KDR in complex with ligand sorafenib · 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 3WZE · PDBe 3WZE · UniProt P35968

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