Research workbench
Crystal structure of human CDK9/CYCLINT1 in complex with MC180295
Analyse Crystal structure of human CDK9/CYCLINT1 in complex with MC180295 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W9E
- Type
- protein
- Length
- 563 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
- TO7, TOJ, PO4
- Pockets
- 12 · best druggability 0.69
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 | 311 | 33% helix, 14% strand | P50750 |
| B | Cyclin-T1 | protein | 252 | 64% helix, 0% strand | O60563 |
Ligands and binding sites
- TO7 · (4-amino-2-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]amino}-1,3-thiazol-5-yl)(2-nitrophenyl)methanone · ligand · 2 copies · chains A
- TOJ · (4-amino-2-{[(1R,2R,4S)-bicyclo[2.2.1]heptan-2-yl]amino}-1,3-thiazol-5-yl)(2-nitrophenyl)methanone · ligand · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.69 | 0.86 | 24 | TO7, TOJ |
| 2 | 111 | 0.59 | 0.86 | 29 | empty |
| 3 | 183 | 0.50 | 0.77 | 24 | empty |
| 4 | 132 | 0.45 | 0.77 | 23 | empty |
| 5 | 90 | 0.44 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 915 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6W9E · Crystal Structure of Human CDK9/cyclinT1 in complex with MC180295 · 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 0.98
- 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 0.97
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 6W9E · PDBe 6W9E · UniProt P50750 · UniProt O60563
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