Research workbench
Structure of CDK2 in complex with cyclin a and a 2-amino-4- heteroaryl-pyrimidine inhibitor
Analyse Structure of CDK2 in complex with cyclin a and a 2-amino-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BCM
- Type
- protein
- Length
- 1,084 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
- T7Z
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 296 | 35% helix, 17% strand | P24941 |
| B | Cyclin-A2 | protein | 257 | 66% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 295 | 34% helix, 18% strand | P24941 |
| D | Cyclin-A2 | protein | 236 | 66% helix, 0% strand | P20248 |
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 · 2 copies · chains A, C
- SGM · Monothioglycerol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.81 | 0.99 | 24 | empty |
| 2 | 120 | 0.80 | 0.99 | 23 | empty |
| 3 | 680 | 0.74 | 0.80 | 61 | empty |
| 4 | 302 | 0.66 | 0.81 | 34 | T7Z |
| 5 | 344 | 0.66 | 0.80 | 35 | T7Z |
Interfaces
5 interfaces between chains.
- C–D · 1683 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1600 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 86 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, phosphorylation).
Compared structures
- 4BCM · Structure of CDK2 in complex with cyclin A and a 2-amino-4-heteroaryl- pyrimidine… · 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 C 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 4BCM · PDBe 4BCM · UniProt P24941 · UniProt P20248
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