Ligand profile

EP1

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

Bound to: VK055_4855 — naphthoate synthase

Via homolog PDB 1rjn UniProt P9WNP5 Formula C₉H₂₀N₂O₄S
Mol. weight 252.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EP1
PDB
1rjn
UniProt (similar protein)
P9WNP5
Target protein
VK055_4855

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 252.34 Da
LogP (Crippen) -1.13
H-bond donors 2
H-bond acceptors 5
TPSA 81.08 Ų
Rotatable bonds 6
Aromatic rings 0 / 1
Heavy atoms 16
Fraction sp³ C 1.00
Formula C₉H₂₀N₂O₄S

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 81.1
  • −1 ≤ LogP ≤ 5 -1.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 252.3
  • LogP ≤ 5 -1.13
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 81.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CN(CCN1CCCS(=O)(=O)O)CCO
InChI 
InChI=1S/C9H20N2O4S/c12-8-7-11-5-3-10(4-6-11)2-1-9-16(13,14)15/h12H,1-9H2,(H,13,14,15)
InChIKey 
OWXMKDGYPWMGEB-UHFFFAOYSA-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
PF00378

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_4855.

PDB 11

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

Ligand PDB entry

ChEMBL 10

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)