Ligand profile

S60

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 3c2y UniProt P28720 Formula C₁₀H₉N₅O
Mol. weight 215.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
S60
PDB
3c2y
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 215.22 Da
LogP (Crippen) 0.69
H-bond donors 3
H-bond acceptors 4
TPSA 100.45 Ų
Rotatable bonds 0
Aromatic rings 3 / 3
Heavy atoms 16
Fraction sp³ C 0.10
Formula C₁₀H₉N₅O

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 100.5
  • −1 ≤ LogP ≤ 5 0.69
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 215.2
  • LogP ≤ 5 0.69
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 100.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1[nH]c2cc3c(cc2n1)N=C(NC3=O)N
InChI 
InChI=1S/C10H9N5O/c1-4-12-7-2-5-6(3-8(7)13-4)14-10(11)15-9(5)16/h2-3H,1H3,(H,12,13)(H3,11,14,15,16)
InChIKey 
PLJNUNPYZVVIRA-UHFFFAOYSA-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
PF01702

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_02055.

PDB 60

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

Ligand PDB entry

ChEMBL 5

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)