Ligand profile

SVS

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

Bound to: KP13_03397 — Isochorismatase

Via homolog PDB 3rg2 UniProt P0ADI4 Formula C₁₈H₂₂N₆O₆S
Mol. weight 450.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SVS
PDB
3rg2
UniProt (similar protein)
P0ADI4
Target protein
KP13_03397

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 450.48 Da
LogP (Crippen) -1.10
H-bond donors 5
H-bond acceptors 11
TPSA 185.71 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 31
Fraction sp³ C 0.39
Formula C₁₈H₂₂N₆O₆S

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 185.7
  • −1 ≤ LogP ≤ 5 -1.10
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 450.5
  • LogP ≤ 5 -1.10
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 185.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(c(c1)CCS(=O)(=O)NC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O
InChI 
InChI=1S/C18H22N6O6S/c19-16-13-17(21-8-20-16)24(9-22-13)18-15(27)14(26)12(30-18)7-23-31(28,29)6-5-10-3-1-2-4-11(10)25/h1-4,8-9,12,14-15,18,23,25-27H,5-7H2,(H2,19,20,21)/t12-,14-,15-,18-/m1/s1
InChIKey 
NIEGSPNRJDKALY-SCFUHWHPSA-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
PF00501

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_03397.

PDB 7

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)