Research workbench
Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor
Analyse Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BCH
- Type
- protein
- Length
- 561 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
- T7Z
- Pockets
- 8 · best druggability 0.66
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 | 309 | 36% helix, 14% strand | P50750 |
| B | Cyclin-T1 | protein | 252 | 66% helix, 0% strand | O60563 |
Ligands and binding sites
- T7Z · 4-(4-methyl-2-methylimino-3H-1,3-thiazol-5-yl)-2-[(4-methyl-3-morpholin-4-ylsulfonyl-phenyl)amino]pyrimidine-5-carbonitrile · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.66 | 0.81 | 39 | T7Z |
| 2 | 135 | 0.64 | 0.87 | 35 | empty |
| 3 | 145 | 0.49 | 0.78 | 20 | empty |
| 4 | 170 | 0.48 | 0.76 | 24 | empty |
| 5 | 138 | 0.45 | 0.77 | 23 | GOL |
Interfaces
1 interface between chains.
- A–B · 923 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4BCH · Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine… · 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 4BCH · PDBe 4BCH · UniProt P50750 · UniProt O60563
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