Ligand profile

9CS

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

Bound to: KP13_31572 — Aminoglycoside N(6')-acetyltransferase

Via homolog PDB 2qir UniProt Q8GLI5 Formula C₁₈H₃₇N₅O₁₀
Mol. weight 483.52 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9CS
PDB
2qir
UniProt (similar protein)
Q8GLI5
Target protein
KP13_31572

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 483.52 Da
LogP (Crippen) -7.33
H-bond donors 11
H-bond acceptors 15
TPSA 288.40 Ų
Rotatable bonds 6
Aromatic rings 0 / 3
Heavy atoms 33
Fraction sp³ C 1.00
Formula C₁₈H₃₇N₅O₁₀

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 288.4
  • −1 ≤ LogP ≤ 5 -7.33
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 483.5
  • LogP ≤ 5 -7.33
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 288.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)N)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)N)N
InChI 
InChI=1S/C18H37N5O10/c19-2-6-11(26)12(27)9(23)17(30-6)32-15-4(20)1-5(21)16(14(15)29)33-18-13(28)8(22)10(25)7(3-24)31-18/h4-18,24-29H,1-3,19-23H2/t4-,5+,6+,7+,8-,9+,10+,11+,12+,13+,14-,15+,16-,17+,18+/m0/s1
InChIKey 
SKKLOUVUUNMCJE-FQSMHNGLSA-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
PF13523

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_31572.

PDB 3

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)