Research workbench
Discovery of a novel, highly potent, and selective THIENO[3,2- D]PYRIMIDINONE-based CDC7 inhibitor with a quinuclidine moiety (tak- 931) as an orally active investigational anti-tumor agent
Analyse Discovery of a novel, highly potent, and selective THIENO[3,2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P5M
- Type
- protein
- Length
- 1,574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho-associated protein kinase 2
- EC
- 2.7.11.1
- UniProt
- O75116
- Ligands
- O1S
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rho-associated protein kinase 2 (EC 2.7.11.1) | protein | 396 | 40% helix, 15% strand | O75116 |
| B | Rho-associated protein kinase 2 (EC 2.7.11.1) | protein | 388 | 40% helix, 14% strand | O75116 |
| C, D | Rho-associated protein kinase 2 (EC 2.7.11.1) | protein | 395 | 40% helix, 14% strand | O75116 |
Ligands and binding sites
- O1S · 6-(5-methyl-1H-pyrazol-4-yl)-2-[(pyrrolidin-1-yl) methyl]thieno[3,2-d]pyrimidin-4(3H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.87 | 0.90 | 77 | empty |
| 2 | 852 | 0.86 | 0.88 | 78 | empty |
| 3 | 766 | 0.83 | 0.86 | 87 | empty |
| 4 | 462 | 0.68 | 0.79 | 57 | O1S |
| 5 | 443 | 0.67 | 0.79 | 44 | O1S |
Interfaces
6 interfaces between chains.
- A–D · 2203 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2096 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 936 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 874 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 674 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6P5M · Discovery of a Novel, Highly Potent, and Selective Thieno[3,2-d]pyrimidi -Based Cdc7… · the same entry in another collection · chain A against A, TM-score 1.00
- O75116 · AlphaFold monomer V2.0 prediction for rho-associated protein kinase 2 (O75116) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O75116
- Elsewhere: RCSB PDB 6P5M · PDBe 6P5M · UniProt O75116
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