Research workbench
Crystal structure of human nima-related kinase 1 (NEK1) with inhibitor.
Analyse Crystal structure of human nima-related kinase 1 (NEK1) with inhibitor. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B9D
- Type
- protein
- Length
- 585 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase NEK1
- EC
- 2.7.11.1
- UniProt
- Q96PY6
- Ligands
- CK7, CL
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase NEK1 (EC 2.7.11.1) | protein | 290 | 42% helix, 16% strand | Q96PY6 |
| B | SERINE/THREONINE-protein kinase NEK1 (EC 2.7.11.1) | protein | 295 | 42% helix, 16% strand | Q96PY6 |
Ligands and binding sites
- CK7 · [4-(2-amino-4-methyl-thiazol-5-yl)-pyrimidin-2-yl]-(3-nitro-phenyl)-amine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.67 | 0.78 | 63 | CK7 |
| 2 | 309 | 0.62 | 0.79 | 42 | CK7 |
| 3 | 55 | 0.58 | 0.91 | 21 | empty |
| 4 | 147 | 0.48 | 0.78 | 23 | CL |
| 5 | 90 | 0.39 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 528 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4B9D · Crystal Structure of Human NIMA-related Kinase 1 (NEK1) with inhibitor. · the same entry in another collection · chain A against A, TM-score 1.00
- Q96PY6 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase NEK1 (Q96PY6) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q96PY6
- Elsewhere: RCSB PDB 4B9D · PDBe 4B9D · UniProt Q96PY6
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