Ligand profile

YY3

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_2065 — cysteine--tRNA ligase

Via homolog UniProt P49589 Formula C₂₈H₃₃N₇O₂
pchembl 7.92 ~12.0 nM
Mol. weight 499.62 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
YY3
UniProt (similar protein)
P49589
pchembl
7.920 (~12.0 nM)
Target protein
VK055_2065

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 499.62 Da
LogP (Crippen) 4.51
H-bond donors 2
H-bond acceptors 8
TPSA 87.55 Ų
Rotatable bonds 10
Aromatic rings 4 / 4
Heavy atoms 37
Fraction sp³ C 0.25
Formula C₂₈H₃₃N₇O₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 87.6
  • −1 ≤ LogP ≤ 5 4.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 499.6
  • LogP ≤ 5 4.51
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 87.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cn1cc(c2c1cccc2)c3ccnc(n3)Nc4cc(c(cc4OC)N(C)CCN(C)C)NC(=O)C=C
InChI 
InChI=1S/C28H33N7O2/c1-7-27(36)30-22-16-23(26(37-6)17-25(22)34(4)15-14-33(2)3)32-28-29-13-12-21(31-28)20-18-35(5)24-11-9-8-10-19(20)24/h7-13,16-18H,1,14-15H2,2-6H3,(H,30,36)(H,29,31,32)
InChIKey 
DUYJMQONPNNFPI-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
ChEMBL
Activity
Uncertain
Binding sites
PF01406

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2065.

PDB 1

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 27

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)