MolNFT v1 · #171419 · protein
CDK9-cyclin-T1 complex bound by compound 24
6Z45 · Cyclin-dependent kinase 9: “CDK9-cyclin-T1 complex bound by compound 24”. X-ray diffraction, 2 ligands (Q6E, PO4), 9 pockets (best druggability 0.66). MolNFT v1 #171419 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z45
- Type
- protein
- Length
- 566 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
- Q6E, PO4
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 47% 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 | 314 | 34% helix, 15% strand | P50750 |
| B | Cyclin-T1 | protein | 252 | 64% helix, 0% strand | O60563 |
Ligands and binding sites
- Q6E · (1~{S},3~{R})-3-acetamido-~{N}-[5-chloranyl-4-(5,5-dimethyl-4,6-dihydropyrrolo[1,2-b]pyrazol-3-yl) pyridin-2-yl]cyclohexane-1-carboxamide · ligand · chains A
- PO4 · Phosphate ion · ion · chains B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.66 | 0.83 | 28 | Q6E |
| 2 | 319 | 0.61 | 0.78 | 35 | empty |
| 3 | 154 | 0.50 | 0.78 | 22 | empty |
| 4 | 83 | 0.48 | 0.82 | 28 | empty |
| 5 | 112 | 0.47 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6Z45 · CDK9-Cyclin-T1 complex bound by compound 24 · the same entry in another collection · chain A against A, TM-score 1.00
- O60563 · AlphaFold monomer V2.0 prediction for cyclin-T1 (O60563) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 0.98
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 6Z45 · PDBe 6Z45 · UniProt P50750 · UniProt O60563
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