Research workbench
Crystal structure of rho-associated protein kinase (ROCK1) with a potent isoquinolone derivative
Analyse Crystal structure of rho-associated protein kinase (ROCK1) with a potent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NDM
- 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 (ROCK1)
- EC
- 2.7.1.37
- UniProt
- Q13464
- Ligands
- 3ND
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rho-associated protein kinase (ROCK1) (EC 2.7.1.37) | protein | 383 | 40% helix, 14% strand | Q13464 |
| B, D | Rho-associated protein kinase (ROCK1) (EC 2.7.1.37) | protein | 396 | 34% helix, 14% strand | Q13464 |
| C | Rho-associated protein kinase (ROCK1) (EC 2.7.1.37) | protein | 371 | 38% helix, 13% strand | Q13464 |
Ligands and binding sites
- 3ND · (3S,4R)-N-(7-chloro-1-oxo-1,4-dihydroisoquinolin-6-yl)-4-(4-chlorophenyl)pyrrolidine-3-carboxamide · ligand · 3 copies · chains 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.74 | 0.77 | 87 | empty |
| 2 | 617 | 0.71 | 0.79 | 68 | 3ND |
| 3 | 342 | 0.67 | 0.81 | 39 | 3ND |
| 4 | 398 | 0.66 | 0.79 | 46 | empty |
| 5 | 382 | 0.66 | 0.79 | 45 | 3ND |
Interfaces
4 interfaces between chains.
- A–B · 2109 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2054 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 441 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 114 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3NDM · Crystal structure of Rho-Associated Protein Kinase (ROCK1) with a potent isoquinolone… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13464 · AlphaFold monomer V2.0 prediction for rho-associated protein kinase 1 (Q13464) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 3NDM · PDBe 3NDM · UniProt Q13464
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