Ligand profile

CHEMBL459679

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt P71716 Formula C₂₁H₂₃N₆NaO₈S
pchembl 6.91 ~123.0 nM
Mol. weight 542.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL459679
UniProt (similar protein)
P71716
pchembl
6.910 (~123.0 nM)
Target protein
VK055_5117

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 542.51 Da
LogP (Crippen) -2.40
H-bond donors 4
H-bond acceptors 13
TPSA 200.09 Ų
Rotatable bonds 8
Aromatic rings 3 / 5
Heavy atoms 37
Fraction sp³ C 0.43
Formula C₂₁H₂₃N₆NaO₈S

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 -2.40
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 542.5
  • LogP ≤ 5 -2.40
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 200.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C([N-]S(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(NC4CCC4)ncnc32)[C@H](O)[C@@H]1O)c1ccccc1O.[Na+]
InChI 
InChI=1S/C21H24N6O8S.Na/c28-13-7-2-1-6-12(13)20(31)26-36(32,33)34-8-14-16(29)17(30)21(35-14)27-10-24-15-18(22-9-23-19(15)27)25-11-4-3-5-11;/h1-2,6-7,9-11,14,16-17,21,29-30H,3-5,8H2,(H3,22,23,25,26,28,31);/q;+1/p-1/t14-,16-,17-,21-;/m1./s1
InChIKey 
JYOSNJSJXONTET-QQAZIOFSSA-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)