Ligand profile

1UD

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 4kwo UniProt P28720 Formula C₁₈H₂₄N₆O₅
Mol. weight 404.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1UD
PDB
4kwo
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 404.43 Da
LogP (Crippen) 0.10
H-bond donors 5
H-bond acceptors 9
TPSA 160.40 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 29
Fraction sp³ C 0.50
Formula C₁₈H₂₄N₆O₅

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 160.4
  • −1 ≤ LogP ≤ 5 0.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 404.4
  • LogP ≤ 5 0.10
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 160.4
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](O4)OC)O)OC)N=C(NC3=O)N
InChI 
InChI=1S/C18H24N6O5/c1-20-18-21-9-6-8-11(22-17(19)24-15(8)26)7(12(9)23-18)4-5-10-14(27-2)13(25)16(28-3)29-10/h6,10,13-14,16,25H,4-5H2,1-3H3,(H2,20,21,23)(H3,19,22,24,26)/t10-,13-,14-,16-/m1/s1
InChIKey 
AYNKUXIALNGELF-DSPGLSBSSA-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)