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X-ray co-structure of rho-associated protein kinase (ROCK1) with a highly selective inhibitor
Analyse X-ray co-structure of rho-associated protein kinase (ROCK1) with a highly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WNF
- Type
- protein
- Length
- 1,535 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
- B4V
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rho-associated protein kinase 1 (EC 2.7.11.1) | protein | 395 | 40% helix, 15% strand | Q13464 |
| B | Rho-associated protein kinase 1 (EC 2.7.11.1) | protein | 358 | 42% helix, 15% strand | Q13464 |
| C | Rho-associated protein kinase 1 (EC 2.7.11.1) | protein | 386 | 39% helix, 15% strand | Q13464 |
| D | Rho-associated protein kinase 1 (EC 2.7.11.1) | protein | 396 | 39% helix, 14% strand | Q13464 |
Ligands and binding sites
- B4V · 1-(4-amino-1,2,5-oxadiazol-3-yl)-5-methyl-N-({3-[(5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridin-2-yl)carbamoyl]phenyl}methyl)-1H-1,2,3-triazole-4-carboxamide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A
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 | 673 | 0.74 | 0.80 | 76 | empty |
| 2 | 400 | 0.68 | 0.81 | 48 | empty |
| 3 | 436 | 0.67 | 0.79 | 45 | B4V |
| 4 | 394 | 0.67 | 0.80 | 36 | B4V |
| 5 | 405 | 0.67 | 0.80 | 38 | B4V |
Interfaces
4 interfaces between chains.
- C–D · 2377 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2171 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 149 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5WNF · X-ray co-structure of rho-associated protein kinase (ROCK1) with a highly selective… · 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 5WNF · PDBe 5WNF · UniProt Q13464
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