Research workbench
Crystal structure of ephrin A2 (EPHA2) receptor protein kinase with compound 2B
Analyse Crystal structure of ephrin A2 (EPHA2) receptor protein kinase with compound 2B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NK2
- Type
- protein
- Length
- 290 residues
- Chains
- 1
- 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
- 8ZZ
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 290 | 42% helix, 17% strand | P29317 |
Ligands and binding sites
- 8ZZ · ~{N}-(2-chloranyl-6-methyl-phenyl)-2-[[3-[[(3~{R}, 4~{R})-3-fluoranylpiperidin-4-yl]carbamoyl]phenyl]amino]-1,3-thiazole-5-carboxamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.73 | 0.80 | 46 | 8ZZ |
| 2 | 75 | 0.35 | 0.76 | 18 | empty |
Compared structures
- 5NK2 · Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 2b · 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 A against A, TM-score 0.95
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 5NK2 · PDBe 5NK2 · UniProt P29317
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