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Complex of the EPHB4 kinase domain with an oxindole inhibitor

Analyse Complex of the EPHB4 kinase domain with an oxindole inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4AW5
Type: protein
Length: 261 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ephrin type-B receptor 4
EC: 2.7.10.1
UniProt: P54760
Ligands: 30K
Pockets: 1 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ephrin type-B receptor 4 (EC 2.7.10.1)	protein	261	43% helix, 18% strand	P54760

Ligands and binding sites

30K · (3Z)-5-[(1-ethylpiperidin-4-yl)amino]-3-[(5-methoxy-1H-benzimidazol-2-yl)(phenyl)methylidene]-1,3-dihydro-2H-indol-2-one · ligand · 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	287	0.60	0.78	30	30K

Compared structures

4AW5 · Complex of the EphB4 kinase domain with an oxindole inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P54760 · AlphaFold monomer V2.0 prediction for ephrin type-B receptor 4 (P54760) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P54760
Elsewhere: RCSB PDB 4AW5 · PDBe 4AW5 · UniProt P54760

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