Ligand profile

3GS

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

Bound to: VK055_1732 — adenosylmethionine-8-amino-7-oxononanoate transaminase

Via homolog PDB 4w1v UniProt P9WQ80 Formula C₁₆H₁₄FNO₅S
Mol. weight 351.36 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3GS
PDB
4w1v
UniProt (similar protein)
P9WQ80
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 351.36 Da
LogP (Crippen) 2.09
H-bond donors 0
H-bond acceptors 6
TPSA 74.60 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.25
Formula C₁₆H₁₄FNO₅S

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 74.6
  • −1 ≤ LogP ≤ 5 2.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 351.4
  • LogP ≤ 5 2.09
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 74.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COC(=O)c1c2n(c(c1C(=O)OC)c3cccc(c3)F)C[S@](=O)C2
InChI 
InChI=1S/C16H14FNO5S/c1-22-15(19)12-11-7-24(21)8-18(11)14(13(12)16(20)23-2)9-4-3-5-10(17)6-9/h3-6H,7-8H2,1-2H3/t24-/m1/s1
InChIKey 
KCIMLJNZZQRAFE-XMMPIXPASA-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
PF00202

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_1732.

PDB 25

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)