MolNFT v1 · #124514 · protein
HCN2 cnbd in complex with cytidine-3', 5'-cyclic monophosphate (ccmp)
5KHG · POTASSIUM/SODIUM hyperpolarization-activated cyclic…: “HCN2 cnbd in complex with cytidine-3', 5'-cyclic monophosphate (ccmp)”. X-ray diffraction, 1 ligand (CC7), 2 pockets (best druggability 0.68). MolNFT v1 #124514 on GenesisL1: 3D…
- PDB
- 5KHG
- Type
- protein
- Length
- 201 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POTASSIUM/SODIUM hyperpolarization-activated cyclic nucleotide-gated channel 2
- UniProt
- O88703
- Ligands
- CC7
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POTASSIUM/SODIUM hyperpolarization-activated cyclic nucleotide-gated channel 2 | protein | 201 | 50% helix, 18% strand | O88703 |
Ligands and binding sites
- CC7 · 4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.68 | 0.88 | 24 | CC7 |
| 2 | 232 | 0.48 | 0.74 | 22 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5KHG · HCN2 CNBD in complex with cytidine-3', 5'-cyclic monophosphate (cCMP) · the same entry in another collection · chain A against A, TM-score 1.00
- O88703 · AlphaFold monomer V2.0 prediction for POTASSIUM/SODIUM hyperpolarization-activated cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O88703
- Elsewhere: RCSB PDB 5KHG · PDBe 5KHG · UniProt O88703
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