Ligand profile

S0N

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

Bound to: VK055_4855 — naphthoate synthase

Via homolog PDB 3t88 UniProt P0ABU0 Formula C₃₂H₄₅N₈O₂₀P₃
Mol. weight 954.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
S0N
PDB
3t88
UniProt (similar protein)
P0ABU0
Target protein
VK055_4855

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 954.67 Da
LogP (Crippen) -1.12
H-bond donors 11
H-bond acceptors 20
TPSA 430.03 Ų
Rotatable bonds 24
Aromatic rings 3 / 4
Heavy atoms 63
Fraction sp³ C 0.50
Formula C₃₂H₄₅N₈O₂₀P₃

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 430.0
  • −1 ≤ LogP ≤ 5 -1.12
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 954.7
  • LogP ≤ 5 -1.12
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 24
  • TPSA ≤ 140 Ų 430.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(=O)O)O
InChI 
InChI=1S/C32H45N8O20P3/c1-32(2,26(45)29(46)36-10-9-22(43)35-12-11-34-21(42)8-7-19(41)17-5-3-4-6-18(17)31(47)48)14-57-63(54,55)60-62(52,53)56-13-20-25(59-61(49,50)51)24(44)30(58-20)40-16-39-23-27(33)37-15-38-28(23)40/h3-6,15-16,20,24-26,30,44-45H,7-14H2,1-2H3,(H,34,42)(H,35,43)(H,36,46)(H,47,48)(H,52,53)(H,54,55)(H2,33,37,38)(H2,49,50,51)/t20-,24-,25-,26+,30-/m1/s1
InChIKey 
QCTNXUGGWNSKFY-HSJNEKGZSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00378

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_4855.

PDB 11

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

Ligand PDB entry

ChEMBL 10

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)