Ligand profile

726

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5lps UniProt P28720 Formula C₂₁H₃₀N₆O₆
Mol. weight 462.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
726
PDB
5lps
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 462.51 Da
LogP (Crippen) 0.77
H-bond donors 4
H-bond acceptors 10
TPSA 158.63 Ų
Rotatable bonds 8
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.57
Formula C₂₁H₃₀N₆O₆

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 158.6
  • −1 ≤ LogP ≤ 5 0.77
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 462.5
  • LogP ≤ 5 0.77
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 158.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1[nH]c2cc3c(c(c2n1)CC[C@@H]4[C@H]([C@@H]([C@H]([C@H](O4)OC)OC)OC)OC)N=C(NC3=O)N
InChI 
InChI=1S/C21H30N6O6/c1-23-21-24-11-8-10-13(25-20(22)27-18(10)28)9(14(11)26-21)6-7-12-15(29-2)16(30-3)17(31-4)19(32-5)33-12/h8,12,15-17,19H,6-7H2,1-5H3,(H2,23,24,26)(H3,22,25,27,28)/t12-,15-,16+,17-,19+/m1/s1
InChIKey 
IXUIMEBGCTWFOR-ZIIYPAMZSA-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)