Research workbench
Optimisation of 6,6-dimethyl pyrrolo 3,4-C pyrazoles: identification of pha-793887, a potent cdk inhibitor suitable for intravenous dosing
Analyse Optimisation of 6,6-dimethyl pyrrolo 3,4-C pyrazoles: identification of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WPA
- Type
- protein
- Length
- 1,113 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- 889, SO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 302 | 33% helix, 18% strand | P24941 |
| B | Cyclin A2 | protein | 258 | 66% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 299 | 35% helix, 18% strand | P24941 |
| D | Cyclin A2 | protein | 254 | 65% helix, 0% strand | P20248 |
Ligands and binding sites
- 889 · N-{6,6-dimethyl-5-[(1-methylpiperidin-4-yl)carbonyl]-1,4,5,6-tetrahydropyrrolo[3,4-c]pyrazol-3-yl}-3-methylbutanamide · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.82 | 0.98 | 24 | empty |
| 2 | 138 | 0.81 | 0.98 | 22 | empty |
| 3 | 719 | 0.76 | 0.81 | 61 | empty |
| 4 | 563 | 0.69 | 0.78 | 63 | empty |
| 5 | 293 | 0.68 | 0.83 | 31 | 889 |
Interfaces
5 interfaces between chains.
- A–B · 1617 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1433 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 537 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 468 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 129 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WPA · Optimisation of 6,6-Dimethyl Pyrrolo 3,4-c pyrazoles: Identification of PHA-793887, a… · 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 D 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 2WPA · PDBe 2WPA · UniProt P24941 · UniProt P20248
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