MolNFT v1 · #86669 · protein
Fragment-based screening identifies a new area for inhibitor binding to checkpoint kinase 2 (CHK2)
4BDK: “Fragment-based screening identifies a new area for inhibitor binding to checkpoint kinase 2 (CHK2)”. X-ray diffraction, 2 ligands (RQQ, NO3), 3 pockets (best druggability 0.57). MolNFT v1 #86669 on GenesisL1: 3D structure, binding…
- PDB
- 4BDK
- Type
- protein
- Length
- 286 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Checkpoint kinase 2
- EC
- 2.7.11.1
- UniProt
- O96017
- Ligands
- RQQ, NO3
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Checkpoint kinase 2 (EC 2.7.11.1) | protein | 286 | 43% helix, 16% strand | O96017 |
Ligands and binding sites
- RQQ · N-[(4-methoxyphenyl)methyl]quinoxaline-6-carboxamide · ligand · chains A
- NO3 · Nitrate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.57 | 0.79 | 29 | RQQ, EDO |
| 2 | 73 | 0.30 | 0.73 | 19 | empty |
| 3 | 55 | 0.26 | 0.73 | 12 | empty |
Compared structures
- 4BDK · Fragment-based screening identifies a new area for inhibitor binding to checkpoint kinase… · the same entry in another collection · chain A against A, TM-score 1.00
- O96017 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase CHK2 (O96017) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 O96017
- Elsewhere: RCSB PDB 4BDK · PDBe 4BDK · UniProt O96017
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