Ligand profile

725

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5lpo UniProt P28720 Formula C₁₉H₂₆N₆O₅
Mol. weight 418.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
725
PDB
5lpo
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 418.45 Da
LogP (Crippen) 0.76
H-bond donors 4
H-bond acceptors 9
TPSA 149.40 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 30
Fraction sp³ C 0.53
Formula C₁₉H₂₆N₆O₅

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 149.4
  • −1 ≤ LogP ≤ 5 0.76
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 418.5
  • LogP ≤ 5 0.76
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 149.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1[nH]c2c(n1)cc3c(c2CC[C@@H]4[C@H]([C@H]([C@@H](O4)OC)OC)OC)N=C(NC3=O)N
InChI 
InChI=1S/C19H26N6O5/c1-21-19-22-10-7-9-12(23-18(20)25-16(9)26)8(13(10)24-19)5-6-11-14(27-2)15(28-3)17(29-4)30-11/h7,11,14-15,17H,5-6H2,1-4H3,(H2,21,22,24)(H3,20,23,25,26)/t11-,14-,15-,17-/m1/s1
InChIKey 
OMBPYCFBGGXDQG-BNGXUDDSSA-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)