MolNFT v1 · #53926 · protein

EPHB4 kinase domain inhibitor complex

2X9F · Ephrin type-B receptor 4: “EPHB4 kinase domain inhibitor complex”. X-ray diffraction, 2 ligands (X9F, MG), 2 pockets (best druggability 0.63). MolNFT v1 #53926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2X9F
Type: protein
Length: 265 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: X9F, MG
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ephrin type-B receptor 4 (EC 2.7.10.1)	protein	265	42% helix, 17% strand	P54760

Ligands and binding sites

X9F · N^4^-1H-indazol-4-yl-N^2^-[3-(methylsulfonyl)phenyl]pyrimidine-2,4-diamine · ligand · chains A
MG · Magnesium ion · metal · 2 copies · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	232	0.63	0.82	27	X9F
2	115	0.63	0.88	27	MG

Compared structures

2X9F · 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 0.97

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 2X9F · PDBe 2X9F · UniProt P54760

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