MolNFT v1 · #90616 · protein
Thr 160 phosphorylated CDK2 H84S, Q85M, K89D - human cyclin A3 complex with the inhibitor RO3306
4EOL · Cyclin-dependent kinase 2: “Thr 160 phosphorylated CDK2 H84S, Q85M, K89D - human cyclin A3 complex with the inhibitor RO3306”. X-ray diffraction, 2 ligands (1RO, MG), 13 pockets (best druggability 0.80). MolNFT v1 #90616 on…
- PDB
- 4EOL
- Type
- protein
- Length
- 1,108 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P20248
- Ligands
- 1RO, MG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 295 | 34% helix, 17% strand | P24941 |
| B | Cyclin-A2 | protein | 257 | 64% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 300 | 34% helix, 16% strand | P24941 |
| D | Cyclin-A2 | protein | 256 | 66% helix, 0% strand | P20248 |
Ligands and binding sites
- 1RO · (5E)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(5H)-one · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains B
- SGM · Monothioglycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.80 | 0.98 | 24 | empty |
| 2 | 115 | 0.80 | 0.98 | 24 | empty |
| 3 | 1046 | 0.73 | 0.76 | 100 | empty |
| 4 | 206 | 0.71 | 0.87 | 23 | 1RO |
| 5 | 199 | 0.69 | 0.87 | 27 | 1RO |
Interfaces
5 interfaces between chains.
- C–D · 1661 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1551 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 549 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 426 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 75 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, phosphorylation).
Compared structures
- 4EOL · Thr 160 phosphorylated CDK2 H84S, Q85M, K89D - 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 4EOL · PDBe 4EOL · UniProt P24941 · UniProt P20248
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