MolNFT v1 · #80117 · protein
CDK9/CYCLIN T in complex with CAN508
3TN8 · Cyclin-dependent kinase 9: “CDK9/CYCLIN T in complex with CAN508”. X-ray diffraction, 2 ligands (F18, PO4), 10 pockets (best druggability 0.70). MolNFT v1 #80117 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3TN8
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 9; Cyclin-T1
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P50750, O60563
- Ligands
- F18, PO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 9 (EC 2.7.11.22, 2.7.11.23) | protein | 305 | 37% helix, 14% strand | P50750 |
| B | Cyclin-T1 | protein | 252 | 63% helix, 0% strand | O60563 |
Ligands and binding sites
- F18 · 4-[(E)-(3,5-diamino-1H-pyrazol-4-yl)diazenyl]phenol · ligand · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains B, A
- GOL · Glycerol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.70 | 0.88 | 24 | F18 |
| 2 | 162 | 0.50 | 0.78 | 20 | empty |
| 3 | 142 | 0.48 | 0.78 | 21 | empty |
| 4 | 102 | 0.45 | 0.79 | 14 | empty |
| 5 | 126 | 0.45 | 0.77 | 20 | GOL |
Interfaces
1 interface between chains.
- A–B · 938 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3TN8 · CDK9/cyclin T in complex with CAN508 · the same entry in another collection · chain A against A, TM-score 1.00
- P50750 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 9 (P50750) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O60563 · AlphaFold monomer V2.0 prediction for cyclin-T1 (O60563) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P50750
- Every structure of UniProt O60563
- Elsewhere: RCSB PDB 3TN8 · PDBe 3TN8 · UniProt P50750 · UniProt O60563
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