Ligand profile

S3P

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_1548 — 3-phosphoshikimate 1-carboxyvinyltransferase

Via homolog PDB 1g6s UniProt P0A6D3 Formula C₇H₁₁O₈P
Mol. weight 254.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
S3P
PDB
1g6s
UniProt (similar protein)
P0A6D3
Target protein
VK055_1548

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 254.13 Da
LogP (Crippen) -1.40
H-bond donors 5
H-bond acceptors 5
TPSA 144.52 Ų
Rotatable bonds 3
Aromatic rings 0 / 1
Heavy atoms 16
Fraction sp³ C 0.57
Formula C₇H₁₁O₈P

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 144.5
  • −1 ≤ LogP ≤ 5 -1.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 254.1
  • LogP ≤ 5 -1.40
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 144.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)OP(=O)(O)O)O)O
InChI 
InChI=1S/C7H11O8P/c8-4-1-3(7(10)11)2-5(6(4)9)15-16(12,13)14/h2,4-6,8-9H,1H2,(H,10,11)(H2,12,13,14)/t4-,5-,6+/m1/s1
InChIKey 
QYOJSKGCWNAKGW-PBXRRBTRSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
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 9

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

Ligand PDB entry

ChEMBL 14

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)