MolNFT v1 · #184015 · protein
Kinase domain of mertk in complex with compound 8
7OAM · Tyrosine-protein kinase mer: “Kinase domain of mertk in complex with compound 8”. X-ray diffraction, 1 ligand (V6H), 5 pockets (best druggability 0.59). MolNFT v1 #184015 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7OAM
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase mer
- EC
- 2.7.10.1
- UniProt
- Q12866
- Ligands
- V6H
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 260 | 42% helix, 17% strand | Q12866 |
| B | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 250 | 39% helix, 19% strand | Q12866 |
Ligands and binding sites
- V6H · 2-[[2,5-bis(fluoranyl)phenyl]methylamino]-4-(cyclopentylamino)-N-[3-(2-oxidanylidenepyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide · ligand · chains B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.59 | 0.76 | 37 | V6H, EDO |
| 2 | 324 | 0.58 | 0.76 | 33 | EDO |
| 3 | 119 | 0.51 | 0.81 | 17 | empty |
| 4 | 245 | 0.49 | 0.74 | 44 | empty |
| 5 | 66 | 0.27 | 0.72 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7OAM · Kinase domain of MERTK in complex with compound 8 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q12866
- Elsewhere: RCSB PDB 7OAM · PDBe 7OAM · UniProt Q12866
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