Ligand profile

5NT

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5egr UniProt P28720 Formula C₁₁H₁₅N₅O₃
Mol. weight 265.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5NT
PDB
5egr
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 265.27 Da
LogP (Crippen) -1.41
H-bond donors 6
H-bond acceptors 6
TPSA 140.05 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.45
Formula C₁₁H₁₅N₅O₃

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 140.1
  • −1 ≤ LogP ≤ 5 -1.41
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 265.3
  • LogP ≤ 5 -1.41
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 140.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c2c([nH]1)C(=O)NC(=N2)N)[C@H]3[C@@H](C[C@H](N3)CO)O
InChI 
InChI=1S/C11H15N5O3/c12-11-15-8-5(2-13-9(8)10(19)16-11)7-6(18)1-4(3-17)14-7/h2,4,6-7,13-14,17-18H,1,3H2,(H3,12,15,16,19)/t4-,6+,7-/m0/s1
InChIKey 
ZIWDWRULEXWPGT-JHYUDYDFSA-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)