MolNFT v1 · #149011 · protein

Crystal structure of ephrin A2 (EPHA2) receptor protein kinase with a PYRAZOLO[3,4-D]PYRIMIDINE fragment of nvp-BHG712

6FNH · Ephrin type-a receptor 2: “Crystal structure of ephrin A2 (EPHA2) receptor protein kinase with a PYRAZOLO[3,4-D]PYRIMIDINE fragment of…”. X-ray diffraction, 1 ligand (DXK), 7 pockets (best druggability 0.69). MolNFT v1 #149011 on…

PDB: 6FNH
Type: protein
Length: 818 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ephrin type-a receptor 2
EC: 2.7.10.1
UniProt: P29317
Ligands: DXK
Pockets: 7 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ephrin type-a receptor 2 (EC 2.7.10.1)	protein	277	41% helix, 17% strand	P29317
B	Ephrin type-a receptor 2 (EC 2.7.10.1)	protein	271	43% helix, 16% strand	P29317
C	Ephrin type-a receptor 2 (EC 2.7.10.1)	protein	270	42% helix, 17% strand	P29317

Ligands and binding sites

DXK · 1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · 3 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	796	0.69	0.76	76	EDO
2	229	0.67	0.85	35	empty
3	294	0.63	0.80	29	DXK
4	319	0.63	0.79	37	DXK, EDO
5	272	0.62	0.80	34	DXK

Interfaces

3 interfaces between chains.

B–C · 569 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 351 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 129 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6FNH · Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with a… · the same entry in another collection · chain A against A, TM-score 1.00
P29317 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 2 (P29317) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P29317
Elsewhere: RCSB PDB 6FNH · PDBe 6FNH · UniProt P29317

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.