MolNFT v1 · #128225 · protein
Crystal structure of ephrin A2 (EPHA2) receptor protein kinase with compound 2C
5NK4 · Ephrin type-a receptor 2: “Crystal structure of ephrin A2 (EPHA2) receptor protein kinase with compound 2C”. X-ray diffraction, 1 ligand (90E), 3 pockets (best druggability 0.71). MolNFT v1 #128225 on GenesisL1: 3D structure…
- PDB
- 5NK4
- 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
- 90E
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 290 | 42% helix, 18% strand | P29317 |
Ligands and binding sites
- 90E · 2-[[3-[[(4~{R})-3,3-bis(fluoranyl)piperidin-4-yl]carbamoyl]phenyl]amino]-~{N}-(2-chloranyl-6-methyl-phenyl)-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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.71 | 0.80 | 44 | 90E |
| 2 | 50 | 0.39 | 0.81 | 16 | empty |
| 3 | 60 | 0.34 | 0.77 | 19 | empty |
Compared structures
- 5NK4 · Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 2c · 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 5NK4 · PDBe 5NK4 · UniProt P29317
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