MolNFT v1 · #182087 · protein
TNNI3K complexed with 1-(3,5-dichloro-4-((6-(METHYLAMINO)PYRIMIDIN-4- YL)OXY)PHENYL)-3-(3-(TRIFLUOROMETHYL)PHENYL)UREA
7MGK · SERINE/THREONINE-protein kinase TNNI3K: “TNNI3K complexed with 1-(3,5-dichloro-4-((6-(METHYLAMINO)PYRIMIDIN-4…”. X-ray diffraction, 1 ligand (ZGD), 11 pockets (best druggability 0.84). MolNFT v1 #182087 on GenesisL1: 3D structure…
- PDB
- 7MGK
- Type
- protein
- Length
- 1,046 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase TNNI3K
- EC
- 2.7.11.1
- UniProt
- Q59H18
- Ligands
- ZGD
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase TNNI3K (EC 2.7.11.1) | protein | 262 | 44% helix, 17% strand | Q59H18 |
| B | SERINE/THREONINE-protein kinase TNNI3K (EC 2.7.11.1) | protein | 261 | 44% helix, 16% strand | Q59H18 |
| C | SERINE/THREONINE-protein kinase TNNI3K (EC 2.7.11.1) | protein | 260 | 43% helix, 16% strand | Q59H18 |
| D | SERINE/THREONINE-protein kinase TNNI3K (EC 2.7.11.1) | protein | 263 | 43% helix, 16% strand | Q59H18 |
Ligands and binding sites
- ZGD · N-(3,5-dichloro-4-{[6-(methylamino)pyrimidin-4-yl]oxy}phenyl)-N'-[3-(trifluoromethyl)phenyl]urea · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.84 | 0.89 | 70 | empty |
| 2 | 423 | 0.72 | 0.82 | 46 | ZGD |
| 3 | 392 | 0.71 | 0.82 | 43 | ZGD |
| 4 | 426 | 0.71 | 0.82 | 46 | ZGD |
| 5 | 440 | 0.71 | 0.81 | 47 | ZGD |
Interfaces
6 interfaces between chains.
- A–B · 2255 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2193 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 676 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 411 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 406 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7MGK · TNNI3K complexed with 1-(3,5-dichloro-4-((6-(methylamino)pyrimidin-4-yl)oxy)phenyl)-3-(3-(… · the same entry in another collection · chain D against D, TM-score 1.00
- Q59H18 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase TNNI3K (Q59H18) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q59H18
- Elsewhere: RCSB PDB 7MGK · PDBe 7MGK · UniProt Q59H18
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