Ligand profile

CHEMBL518346

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_5117 — 2,3-dihydroxybenzoate-AMP ligase

Via homolog UniProt P71716 Formula C₁₈H₁₉N₆NaO₈S
pchembl 8.80 ~1.6 nM
Mol. weight 502.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL518346
UniProt (similar protein)
P71716
pchembl
8.800 (~1.6 nM)
Target protein
VK055_5117

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 502.44 Da
LogP (Crippen) -3.33
H-bond donors 4
H-bond acceptors 13
TPSA 200.09 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 34
Fraction sp³ C 0.33
Formula C₁₈H₁₉N₆NaO₈S

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 200.1
  • −1 ≤ LogP ≤ 5 -3.33
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 502.4
  • LogP ≤ 5 -3.33
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 200.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1ncnc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)[N-]C(=O)c2ccccc2O)[C@@H](O)[C@H]1O.[Na+]
InChI 
InChI=1S/C18H20N6O8S.Na/c1-19-15-12-16(21-7-20-15)24(8-22-12)18-14(27)13(26)11(32-18)6-31-33(29,30)23-17(28)9-4-2-3-5-10(9)25;/h2-5,7-8,11,13-14,18,26-27H,6H2,1H3,(H3,19,20,21,23,25,28);/q;+1/p-1/t11-,13-,14-,18-;/m1./s1
InChIKey 
JMHSYKWHKSYENO-CATZXYISSA-M

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00501' 'PF13193

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_5117.

PDB 7

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

Ligand PDB entry

ChEMBL 81

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)