MolNFT v1 · #5161 · protein
Thr 160 phosphorylated CDK2 - human cyclin A3 complex with the inhibitor indirubin-5-sulphonate bound
1E9H · Cell division protein kinase 2: “Thr 160 phosphorylated CDK2 - human cyclin A3 complex with the inhibitor indirubin-5-sulphonate bound”. X-ray diffraction, 1 ligand (INR), 9 pockets (best druggability 0.81). MolNFT v1 #5161 on…
- PDB
- 1E9H
- Type
- protein
- Length
- 1,109 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A3
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- INR
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 296 | 33% helix, 16% strand | P24941 |
| B, D | Cyclin A3 | protein | 258 | 66% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 297 | 34% helix, 15% strand | P24941 |
Ligands and binding sites
- INR · 2',3-dioxo-1,1',2',3-tetrahydro-2,3'-biindole-5'-sulfonic acid · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.81 | 0.99 | 21 | empty |
| 2 | 122 | 0.80 | 0.98 | 22 | empty |
| 3 | 389 | 0.70 | 0.82 | 39 | INR |
| 4 | 316 | 0.67 | 0.81 | 37 | INR |
| 5 | 296 | 0.62 | 0.80 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1795 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1786 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1E9H · Thr 160 phosphorylated CDK2 - Human cyclin A3 complex with the inhibitor… · the same entry in another collection · chain D against D, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P24941
- Every structure of UniProt P20248
- Elsewhere: RCSB PDB 1E9H · PDBe 1E9H · UniProt P24941 · UniProt P20248
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