Ligand profile

PK2

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 3eos UniProt P28720 Formula C₁₉H₂₇N₇O
Mol. weight 369.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PK2
PDB
3eos
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 369.47 Da
LogP (Crippen) 2.14
H-bond donors 5
H-bond acceptors 6
TPSA 124.51 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 27
Fraction sp³ C 0.53
Formula C₁₉H₂₇N₇O

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 124.5
  • −1 ≤ LogP ≤ 5 2.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 369.5
  • LogP ≤ 5 2.14
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 124.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1[nH]c2cc3c(c(c2n1)CCNCC4CCCCC4)N=C(NC3=O)N
InChI 
InChI=1S/C19H27N7O/c1-21-19-23-14-9-13-15(24-18(20)26-17(13)27)12(16(14)25-19)7-8-22-10-11-5-3-2-4-6-11/h9,11,22H,2-8,10H2,1H3,(H2,21,23,25)(H3,20,24,26,27)
InChIKey 
ZKRVOXSNLYAMLM-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)