MolNFT v1 · #59044 · protein
Crystal structure of human CDK9/CYCLINT1 in complex with flavopiridol
3BLR · Cell division protein kinase 9: “Crystal structure of human CDK9/CYCLINT1 in complex with flavopiridol”. X-ray diffraction, 2 ligands (CPB, PO4), 11 pockets (best druggability 0.65). MolNFT v1 #59044 on GenesisL1: 3D structure…
- PDB
- 3BLR
- Type
- protein
- Length
- 552 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
- CPB, PO4
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 8% 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 | 301 | 36% helix, 15% strand | P50750 |
| B | Cyclin-T1 | protein | 251 | 63% helix, 0% strand | O60563 |
Ligands and binding sites
- CPB · 2-(2-chloro-phenyl)-5,7-dihydroxy-8-(3-hydroxy-1-methyl-piperidin-4-yl)-4H-benzopyran-4-one · ligand · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.65 | 0.84 | 23 | CPB |
| 2 | 63 | 0.48 | 0.85 | 21 | empty |
| 3 | 155 | 0.48 | 0.77 | 20 | empty |
| 4 | 114 | 0.47 | 0.79 | 24 | empty |
| 5 | 135 | 0.47 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 921 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3BLR · Crystal Structure of Human CDK9/cyclinT1 in complex with Flavopiridol · 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 3BLR · PDBe 3BLR · UniProt P50750 · UniProt O60563
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