Ligand profile

1WK

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 4leq UniProt P28720 Formula C₁₇H₂₂N₆O₅
Mol. weight 390.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1WK
PDB
4leq
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 390.40 Da
LogP (Crippen) -0.55
H-bond donors 6
H-bond acceptors 9
TPSA 171.40 Ų
Rotatable bonds 5
Aromatic rings 3 / 4
Heavy atoms 28
Fraction sp³ C 0.47
Formula C₁₇H₂₂N₆O₅

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 171.4
  • −1 ≤ LogP ≤ 5 -0.55
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 390.4
  • LogP ≤ 5 -0.55
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 171.4
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)O)N=C(NC3=O)N
InChI 
InChI=1S/C17H22N6O5/c1-19-17-20-8-5-7-10(21-16(18)23-14(7)26)6(11(8)22-17)3-4-9-12(24)13(25)15(27-2)28-9/h5,9,12-13,15,24-25H,3-4H2,1-2H3,(H2,19,20,22)(H3,18,21,23,26)/t9-,12-,13-,15-/m1/s1
InChIKey 
VKQAJTKFJIETGO-QGMIFYJMSA-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)