Ligand profile

S2N

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

Bound to: KP13_01800 — UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase

Via homolog PDB 3i3a UniProt Q8EZA6 Formula C₂₄H₄₇N₂O₉PS
Mol. weight 570.69 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
S2N
PDB
3i3a
UniProt (similar protein)
Q8EZA6
Target protein
KP13_01800

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 570.69 Da
LogP (Crippen) 2.91
H-bond donors 5
H-bond acceptors 9
TPSA 171.49 Ų
Rotatable bonds 22
Aromatic rings 0 / 0
Heavy atoms 37
Fraction sp³ C 0.88
Formula C₂₄H₄₇N₂O₉PS

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 171.5
  • −1 ≤ LogP ≤ 5 2.91
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 570.7
  • LogP ≤ 5 2.91
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 22
  • TPSA ≤ 140 Ų 171.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCC[C@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@@](=O)(O)OC)O)O
InChI 
InChI=1S/C24H47N2O9PS/c1-5-6-7-8-9-10-11-12-19(27)17-21(29)37-16-15-25-20(28)13-14-26-23(31)22(30)24(2,3)18-35-36(32,33)34-4/h19,22,27,30H,5-18H2,1-4H3,(H,25,28)(H,26,31)(H,32,33)/t19-,22+/m1/s1
InChIKey 
RYLXPSVPJNKBKQ-KNQAVFIVSA-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
PF00132' 'PF13720

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_01800.

PDB 17

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)