Ligand profile

2YM

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 4q4o UniProt P28720 Formula C₁₆H₂₁N₇O
Mol. weight 327.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2YM
PDB
4q4o
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 327.39 Da
LogP (Crippen) 1.28
H-bond donors 4
H-bond acceptors 6
TPSA 115.72 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 24
Fraction sp³ C 0.44
Formula C₁₆H₂₁N₇O

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 115.7
  • −1 ≤ LogP ≤ 5 1.28
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 327.4
  • LogP ≤ 5 1.28
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 115.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c2c(cc3c1nc([nH]3)NCCN4CCCCC4)NC(=NC2=O)N
InChI 
InChI=1S/C16H21N7O/c17-15-19-11-9-13-12(8-10(11)14(24)22-15)20-16(21-13)18-4-7-23-5-2-1-3-6-23/h8-9H,1-7H2,(H2,18,20,21)(H3,17,19,22,24)
InChIKey 
BIGVTSCIEIRKFZ-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)