Ligand profile

L9X

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

Bound to: VK055_3738 — proton antiporter-2 family protein

Via homolog PDB 3l9x UniProt P03819 Formula C₁₆H₂₄N₄O₈S
Mol. weight 432.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
L9X
PDB
3l9x
UniProt (similar protein)
P03819
Target protein
VK055_3738

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 432.46 Da
LogP (Crippen) -2.26
H-bond donors 5
H-bond acceptors 8
TPSA 196.20 Ų
Rotatable bonds 12
Aromatic rings 0 / 1
Heavy atoms 29
Fraction sp³ C 0.62
Formula C₁₆H₂₄N₄O₈S

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 196.2
  • −1 ≤ LogP ≤ 5 -2.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 432.5
  • LogP ≤ 5 -2.26
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 196.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCN1C(=O)C[C@H](C1=O)SC[C@@H](C(=O)NCC(=O)O)NC(=O)CCC(C(=O)O)N
InChI 
InChI=1S/C16H24N4O8S/c1-2-20-12(22)5-10(15(20)26)29-7-9(14(25)18-6-13(23)24)19-11(21)4-3-8(17)16(27)28/h8-10H,2-7,17H2,1H3,(H,18,25)(H,19,21)(H,23,24)(H,27,28)/t8?,9-,10+/m0/s1
InChIKey 
QCPAUAAIPLHRLB-CBMCFHRWSA-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
PF02254

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_3738.

PDB 3

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)