MolNFT v1 · #159932 · protein
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
6P5P · Rho-associated protein kinase 2: “Discovery of a novel, highly potent, and selective THIENO[3,2- D]PYRIMIDINONE-based CDC7 inhibitor with a…”. X-ray diffraction, 1 ligand (O1V), 18 pockets (best druggability 0.83). MolNFT v1 #159932…
- PDB
- 6P5P
- Type
- protein
- Length
- 1,512 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
- O1V
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rho-associated protein kinase 2 (EC 2.7.11.1) | protein | 386 | 40% helix, 13% strand | O75116 |
| B | Rho-associated protein kinase 2 (EC 2.7.11.1) | protein | 369 | 41% helix, 14% strand | O75116 |
| C | Rho-associated protein kinase 2 (EC 2.7.11.1) | protein | 375 | 39% helix, 13% strand | O75116 |
| D | Rho-associated protein kinase 2 (EC 2.7.11.1) | protein | 382 | 39% helix, 13% strand | O75116 |
Ligands and binding sites
- O1V · 2-[(2S)-1-azabicyclo[2.2.2]octan-2-yl]-6-(5-methyl-1H-pyrazol-4-yl)thieno[3,2-d]pyrimidin-4(3H)-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.83 | 0.84 | 86 | empty |
| 2 | 1196 | 0.81 | 0.82 | 96 | empty |
| 3 | 1034 | 0.74 | 0.77 | 88 | empty |
| 4 | 418 | 0.67 | 0.80 | 42 | O1V |
| 5 | 398 | 0.66 | 0.80 | 40 | O1V |
Interfaces
6 interfaces between chains.
- A–D · 1906 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1702 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 879 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 877 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 266 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6P5P · Discovery of a Novel, Highly Potent, and Selective Thieno[3,2-d]pyrimidi -Based Cdc7… · the same entry in another collection · chain D against D, 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 D 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 6P5P · PDBe 6P5P · UniProt O75116
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