Research workbench
Structure of CDK9/CYCLINT in complex with S-CR8
Analyse Structure of CDK9/CYCLINT in complex with S-CR8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LQ5
- Type
- protein
- Length
- 559 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 9; Cyclin-T1
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P50750, O60563
- Ligands
- SLQ
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 9 (EC 2.7.11.22, 2.7.11.23) | protein | 308 | 34% helix, 16% strand | P50750 |
| B | Cyclin-T1 | protein | 251 | 64% helix, 0% strand | O60563 |
Ligands and binding sites
- SLQ · (2S)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.65 | 0.83 | 26 | SLQ |
| 2 | 158 | 0.50 | 0.78 | 20 | empty |
| 3 | 60 | 0.47 | 0.84 | 21 | empty |
| 4 | 97 | 0.45 | 0.79 | 15 | empty |
| 5 | 114 | 0.42 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 917 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3LQ5 · Structure of CDK9/CyclinT in complex with S-CR8 · 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 3LQ5 · PDBe 3LQ5 · UniProt P50750 · UniProt O60563
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.