Ligand profile

CHEMBL516501

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt P71716 Formula C₁₉H₂₁N₆NaO₈S
pchembl 8.36 ~4.4 nM
Mol. weight 516.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL516501
UniProt (similar protein)
P71716
pchembl
8.360 (~4.4 nM)
Target protein
VK055_5117

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 516.47 Da
LogP (Crippen) -2.94
H-bond donors 4
H-bond acceptors 13
TPSA 200.09 Ų
Rotatable bonds 8
Aromatic rings 3 / 4
Heavy atoms 35
Fraction sp³ C 0.37
Formula C₁₉H₂₁N₆NaO₈S

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 -2.94
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 516.5
  • LogP ≤ 5 -2.94
  • 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 
CCNc1ncnc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)[N-]C(=O)c2ccccc2O)[C@@H](O)[C@H]1O.[Na+]
InChI 
InChI=1S/C19H22N6O8S.Na/c1-2-20-16-13-17(22-8-21-16)25(9-23-13)19-15(28)14(27)12(33-19)7-32-34(30,31)24-18(29)10-5-3-4-6-11(10)26;/h3-6,8-9,12,14-15,19,27-28H,2,7H2,1H3,(H3,20,21,22,24,26,29);/q;+1/p-1/t12-,14-,15-,19-;/m1./s1
InChIKey 
OPDLKMWWTUCRIU-CAUXPVPNSA-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)