Ligand profile

CHEMBL313253

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_1548 — 3-phosphoshikimate 1-carboxyvinyltransferase

Via homolog UniProt P0A6D3 Formula C₉H₆Na₄O₁₂P₂
pchembl 6.80 ~158.5 nM
Mol. weight 460.04 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL313253
UniProt (similar protein)
P0A6D3
pchembl
6.800 (~158.5 nM)
Target protein
VK055_1548

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 460.04 Da
LogP (Crippen) -16.09
H-bond donors 2
H-bond acceptors 10
TPSA 219.44 Ų
Rotatable bonds 7
Aromatic rings 1 / 1
Heavy atoms 27
Fraction sp³ C 0.11
Formula C₉H₆Na₄O₁₂P₂

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 219.4
  • −1 ≤ LogP ≤ 5 -16.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 460.0
  • LogP ≤ 5 -16.09
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 219.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C([O-])c1cc(OC(C(=O)[O-])P(=O)([O-])O)cc(OP(=O)([O-])O)c1.[Na+].[Na+].[Na+].[Na+]
InChI 
InChI=1S/C9H10O12P2.4Na/c10-7(11)4-1-5(3-6(2-4)21-23(17,18)19)20-9(8(12)13)22(14,15)16;;;;/h1-3,9H,(H,10,11)(H,12,13)(H2,14,15,16)(H2,17,18,19);;;;/q;4*+1/p-4
InChIKey 
GOMCBQZQHUNFIH-UHFFFAOYSA-J

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Binding sites
PF00275

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_1548.

PDB 10

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

Ligand PDB entry

ChEMBL 13

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)