Ligand profile

ON0

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

Bound to: KP13_31772 — 30S ribosomal protein S12

Via homolog PDB 4b3m UniProt Q5SHN3 Formula C₃₀H₄₉N₅O₁₄
Mol. weight 703.74 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ON0
PDB
4b3m
UniProt (similar protein)
Q5SHN3
Target protein
KP13_31772

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 703.74 Da
LogP (Crippen) -6.10
H-bond donors 11
H-bond acceptors 19
TPSA 325.32 Ų
Rotatable bonds 9
Aromatic rings 1 / 6
Heavy atoms 49
Fraction sp³ C 0.80
Formula C₃₀H₄₉N₅O₁₄

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 325.3
  • −1 ≤ LogP ≤ 5 -6.10
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 703.7
  • LogP ≤ 5 -6.10
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 325.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)[C@@H]2OC[C@@H]3[C@@H](O2)[C@@H]([C@H]([C@H](O3)O[C@@H]4[C@H](C[C@H]([C@@H]([C@H]4O[C@H]5[C@@H]([C@@H]([C@H](O5)CO)O[C@@H]6[C@@H]([C@H]([C@@H]([C@@H](O6)CN)O)O)N)O)O)N)N)N)O
InChI 
InChI=1S/C30H49N5O14/c31-7-13-19(38)20(39)16(34)28(43-13)48-24-14(8-36)44-30(22(24)41)49-26-18(37)11(32)6-12(33)23(26)46-29-17(35)21(40)25-15(45-29)9-42-27(47-25)10-4-2-1-3-5-10/h1-5,11-30,36-41H,6-9,31-35H2/t11-,12+,13+,14-,15-,16-,17-,18+,19-,20-,21-,22-,23-,24-,25-,26-,27-,28-,29-,30+/m1/s1
InChIKey 
BJNRNAHKVYQUCR-CQXNUXSXSA-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
PF00164

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_31772.

PDB 12

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

Ligand PDB entry

ChEMBL 2

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)