Ligand profile

CHEMBL1506682

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_4127 — phosphoglycerate kinase family protein

Via homolog UniProt P07378 Formula C₂₁H₁₈O₁₃
Mol. weight 478.36 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1506682
UniProt (similar protein)
P07378
Target protein
VK055_4127

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 478.36 Da
LogP (Crippen) -0.45
H-bond donors 8
H-bond acceptors 12
TPSA 227.58 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 34
Fraction sp³ C 0.24
Formula C₂₁H₁₈O₁₃

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 227.6
  • −1 ≤ LogP ≤ 5 -0.45
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 478.4
  • LogP ≤ 5 -0.45
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 227.6
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)C1OC(Oc2c(-c3ccc(O)c(O)c3)oc3cc(O)cc(O)c3c2=O)C(O)C(O)C1O
InChI 
InChI=1S/C21H18O13/c22-7-4-10(25)12-11(5-7)32-17(6-1-2-8(23)9(24)3-6)18(13(12)26)33-21-16(29)14(27)15(28)19(34-21)20(30)31/h1-5,14-16,19,21-25,27-29H,(H,30,31)
InChIKey 
DUBCCGAQYVUYEU-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
ChEMBL
Activity
active
Binding sites
PF00162

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_4127.

PDB 4

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

Ligand PDB entry

ChEMBL 99

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)