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General structure-based approach to the design of protein ligands: application to the design of KV1.2 potassium channel blockers.

Analyse General structure-based approach to the design of protein ligands: application… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2HEO
Type
protein + DNA
Length
129 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*TP*CP*GP*CP*GP*CP*G)-3'; Z-DNA binding protein 1
UniProt
Q9QY24
Pockets
1 · best druggability 0.44

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 16% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B, E5'-D(*TP*CP*GP*CP*GP*CP*G)-3'dna6——
AZ-DNA binding protein 1protein5958% helix, 19% strandQ9QY24
DZ-DNA binding protein 1protein5855% helix, 14% strandQ9QY24

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11690.440.7516empty

Interfaces

3 interfaces between chains.

  • B–E · 324 Ų buried · 24 hydrogen bonds · nucleic-nucleic
  • B–A · 320 Ų buried · 4 hydrogen bonds · protein-nucleic
  • E–D · 316 Ų buried · 5 hydrogen bonds · protein-nucleic

Compared structures

  • 2HEO · General Structure-Based Approach to the Design of Protein Ligands: Application to the… · the same entry in another collection · chain B against B, TM-score 1.00
  • Q9QY24 · AlphaFold monomer V2.0 prediction for Z-DNA-binding protein 1 (Q9QY24) · a predicted model of the same protein · chain D against A, TM-score 0.96

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