Ligand profile

1KM

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

Bound to: VK055_2682 — glutathione transferase fosA

Via homolog PDB 4jh7 UniProt Q739M9 Formula C₆H₁₄NO₆PS
Mol. weight 259.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1KM
PDB
4jh7
UniProt (similar protein)
Q739M9
Target protein
VK055_2682

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 259.22 Da
LogP (Crippen) -0.98
H-bond donors 5
H-bond acceptors 5
TPSA 141.08 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 15
Fraction sp³ C 0.83
Formula C₆H₁₄NO₆PS

Drug-likeness

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

Permeability proxy Check

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 141.1
  • −1 ≤ LogP ≤ 5 -0.98
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 259.2
  • LogP ≤ 5 -0.98
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 141.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]([C@H](P(=O)(O)O)SC[C@@H](C(=O)O)N)O
InChI 
InChI=1S/C6H14NO6PS/c1-3(8)6(14(11,12)13)15-2-4(7)5(9)10/h3-4,6,8H,2,7H2,1H3,(H,9,10)(H2,11,12,13)/t3-,4-,6+/m0/s1
InChIKey 
ACZNEKUZDVGTFM-RVJQKOHUSA-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
PF00903

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_2682.

PDB 5

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

Ligand PDB entry

ZINC 20

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

Compound Similarity (Tanimoto)