MolNFT v1 · #84321 · protein
A novel small molecule apkc inhibitor
3ZH8 · Protein kinase C iota type: “A novel small molecule apkc inhibitor”. X-ray diffraction, 3 ligands (C58, IOD, CL), 17 pockets (best druggability 0.65). MolNFT v1 #84321 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZH8
- Type
- protein
- Length
- 953 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase C iota type
- EC
- 2.7.11.13
- UniProt
- P41743
- Ligands
- C58, IOD, CL
- Pockets
- 17 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein kinase C iota type (EC 2.7.11.13) | protein | 320 | 38% helix, 17% strand | P41743 |
| B | Protein kinase C iota type (EC 2.7.11.13) | protein | 319 | 38% helix, 17% strand | P41743 |
| C | Protein kinase C iota type (EC 2.7.11.13) | protein | 314 | 38% helix, 17% strand | P41743 |
Ligands and binding sites
- C58 · (2S)-3-phenyl-N~1~-[2-(pyridin-4-yl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-yl]propane-1,2-diamine · ligand · 3 copies · chains A, B, C
- IOD · Iodide ion · ion · 12 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.65 | 0.82 | 29 | C58, EDO |
| 2 | 260 | 0.65 | 0.82 | 27 | IOD, C58 |
| 3 | 269 | 0.64 | 0.81 | 30 | IOD, C58 |
| 4 | 358 | 0.61 | 0.78 | 37 | empty |
| 5 | 111 | 0.51 | 0.81 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–B · 426 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 224 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
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 P41743
- Elsewhere: RCSB PDB 3ZH8 · PDBe 3ZH8 · UniProt P41743
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