Research workbench
Human rho-associated protein kinase 1 (rock 1) in complex with indazole derivative (compound 18)
Analyse Human rho-associated protein kinase 1 (rock 1) in complex with indazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V8S
- Type
- protein
- Length
- 1,584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho-associated protein kinase 1
- EC
- 2.7.11.1
- UniProt
- Q13464
- Ligands
- 0HD
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Rho-associated protein kinase 1 (EC 2.7.11.1) | protein | 395 | 41% helix, 15% strand | Q13464 |
| B, D | Rho-associated protein kinase 1 (EC 2.7.11.1) | protein | 397 | 40% helix, 14% strand | Q13464 |
Ligands and binding sites
- 0HD · 1-(1H-indazol-5-yl)-3-(2-phenylethyl)urea · ligand · 4 copies · chains A, B, C, D
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 | 566 | 0.74 | 0.81 | 68 | empty |
| 2 | 502 | 0.70 | 0.80 | 60 | empty |
| 3 | 404 | 0.69 | 0.81 | 45 | 0HD |
| 4 | 479 | 0.68 | 0.79 | 56 | 0HD |
| 5 | 493 | 0.68 | 0.79 | 55 | 0HD |
Interfaces
3 interfaces between chains.
- C–D · 1943 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1937 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 243 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3V8S · Human RHO-ASSOCIATED PROTEIN KINASE 1 (ROCK 1) IN COMPLEX WITH INDAZOLE DERIVATIVE… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q13464
- Elsewhere: RCSB PDB 3V8S · PDBe 3V8S · UniProt Q13464
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