Ligand profile

K1U

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

Bound to: VK055_3786 — peptide deformylase

Via homolog PDB 6jeu UniProt B0VNL8 Formula C₁₉H₁₈O₄S
Mol. weight 342.42 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K1U
PDB
6jeu
UniProt (similar protein)
B0VNL8
Target protein
VK055_3786

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 342.42 Da
LogP (Crippen) 3.46
H-bond donors 1
H-bond acceptors 4
TPSA 71.44 Ų
Rotatable bonds 8
Aromatic rings 2 / 2
Heavy atoms 24
Fraction sp³ C 0.21
Formula C₁₉H₁₈O₄S

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 71.4
  • −1 ≤ LogP ≤ 5 3.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 342.4
  • LogP ≤ 5 3.46
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 71.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C[C@H](CC(=O)O)C(=O)SCC(=O)c2ccccc2
InChI 
InChI=1S/C19H18O4S/c20-17(15-9-5-2-6-10-15)13-24-19(23)16(12-18(21)22)11-14-7-3-1-4-8-14/h1-10,16H,11-13H2,(H,21,22)/t16-/m1/s1
InChIKey 
XBDWLLDIBQGWMW-MRXNPFEDSA-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
PF01327

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_3786.

PDB 11

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

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)