Ligand profile

6H9

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5j9n UniProt P28720 Formula C₉H₁₁N₅O
Mol. weight 205.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6H9
PDB
5j9n
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 205.22 Da
LogP (Crippen) 0.21
H-bond donors 4
H-bond acceptors 4
TPSA 95.83 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 15
Fraction sp³ C 0.11
Formula C₉H₁₁N₅O

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 95.8
  • −1 ≤ LogP ≤ 5 0.21
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 205.2
  • LogP ≤ 5 0.21
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 95.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1[nH]c2ccc(cc2n1)C(=O)NN
InChI 
InChI=1S/C9H11N5O/c1-11-9-12-6-3-2-5(8(15)14-10)4-7(6)13-9/h2-4H,10H2,1H3,(H,14,15)(H2,11,12,13)
InChIKey 
UAYYHYYNSIPFPB-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)