Research workbench
Identification of a new class of potent CDC7 inhibitors designed by putative pharmacophore model: synthesis and biological evaluation of 2,3-DIHYDROTHIENO[3,2-D]PYRIMIDIN-4(1H)-ones
Analyse Identification of a new class of potent CDC7 inhibitors designed by putative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U7Q
- Type
- protein
- Length
- 1,546 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
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 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 | 388 | 41% helix, 14% strand | O75116 |
| B | Rho-associated protein kinase 2 (EC 2.7.11.1) | protein | 385 | 40% helix, 15% strand | O75116 |
| C | Rho-associated protein kinase 2 (EC 2.7.11.1) | protein | 390 | 41% helix, 15% strand | O75116 |
| D | Rho-associated protein kinase 2 (EC 2.7.11.1) | protein | 383 | 40% helix, 14% strand | O75116 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.79 | 0.80 | 72 | empty |
| 2 | 559 | 0.71 | 0.80 | 61 | empty |
| 3 | 530 | 0.69 | 0.79 | 44 | empty |
| 4 | 513 | 0.68 | 0.78 | 55 | empty |
| 5 | 487 | 0.67 | 0.78 | 57 | empty |
Interfaces
4 interfaces between chains.
- A–D · 515 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 511 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 429 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 392 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5U7Q · Identification of A New Class of Potent Cdc7 Inhibitors Designed by Putative… · 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 5U7Q · PDBe 5U7Q · UniProt O75116
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