MolNFT v1 · #52308 · protein

EPHB4 kinase domain inhibitor complex

2VWW · Ephrin type-B receptor 4: “EPHB4 kinase domain inhibitor complex”. X-ray diffraction, 1 ligand (7X2), 1 pocket (best druggability 0.59). MolNFT v1 #52308 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VWW
Type: protein
Length: 253 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: 7X2
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ephrin type-B receptor 4 (EC 2.7.10.1)	protein	253	44% helix, 17% strand	P54760

Ligands and binding sites

7X2 · N'-(5-chloro-1,3-benzodioxol-4-yl)-N-(3,4,5- trimethoxyphenyl)pyrimidine-2,4-diamine · 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	221	0.59	0.80	26	7X2

Compared structures

2VWW · ephB4 kinase domain inhibitor complex · 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 2VWW · PDBe 2VWW · UniProt P54760

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