Research workbench
Crystal structure of the human LIMK2 kinase domain in complex with a non-ATP competitive inhibitor
Analyse Crystal structure of the human LIMK2 kinase domain in complex with a non-ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TPT
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lim domain kinase 2
- EC
- 2.7.11.1
- UniProt
- P53671
- Ligands
- 35H
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lim domain kinase 2 (EC 2.7.11.1) | protein | 279 | 38% helix, 18% strand | P53671 |
| B | Lim domain kinase 2 (EC 2.7.11.1) | protein | 277 | 39% helix, 17% strand | P53671 |
Ligands and binding sites
- 35H · N-{4-[(1S)-1,2-dihydroxyethyl]benzyl}-N-methyl-4-(phenylsulfamoyl)benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.83 | 0.88 | 90 | 35H |
| 2 | 233 | 0.80 | 0.92 | 28 | 35H |
| 3 | 128 | 0.54 | 0.82 | 18 | empty |
| 4 | 67 | 0.52 | 0.86 | 19 | empty |
| 5 | 118 | 0.49 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2372 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4TPT · Crystal Structure of the Human LIMK2 Kinase Domain In Complex With a Non-ATP Competitive… · the same entry in another collection · chain A against A, TM-score 1.00
- P53671 · AlphaFold monomer V2.0 prediction for lim domain kinase 2 (P53671) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P53671
- Elsewhere: RCSB PDB 4TPT · PDBe 4TPT · UniProt P53671
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