Ligand profile

3PK

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_3425 — putative efflux pump outer membrane protein ttgC

Via homolog PDB 4k7r UniProt P77211 Formula C₁₄H₂₆O₄
Mol. weight 258.36 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3PK
PDB
4k7r
UniProt (similar protein)
P77211
Target protein
VK055_3425

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 258.36 Da
LogP (Crippen) 3.23
H-bond donors 0
H-bond acceptors 4
TPSA 52.60 Ų
Rotatable bonds 10
Aromatic rings 0 / 0
Heavy atoms 18
Fraction sp³ C 0.86
Formula C₁₄H₂₆O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 52.6
  • −1 ≤ LogP ≤ 5 3.23
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 258.4
  • LogP ≤ 5 3.23
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 52.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCC(=O)O[C@@H](C)COC(=O)CCCC
InChI 
InChI=1S/C14H26O4/c1-4-6-8-10-14(16)18-12(3)11-17-13(15)9-7-5-2/h12H,4-11H2,1-3H3/t12-/m0/s1
InChIKey 
XIGVTLHUQMMWJT-LBPRGKRZSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF02321

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3425.

PDB 4

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)