Ligand profile

ZINC1911936317

Virtual-screening candidate from ZINC.

Bound to: VK055_2065 — cysteine--tRNA ligase

Via homolog UniProt P49589 Formula C₂₇H₃₀N₆O₃
Tanimoto 0.82
Mol. weight 486.58 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1911936317
UniProt (similar protein)
P49589
Tanimoto
0.818
Target protein
VK055_2065

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 486.58 Da
LogP (Crippen) 4.45
H-bond donors 2
H-bond acceptors 8
TPSA 93.54 Ų
Rotatable bonds 10
Aromatic rings 4 / 4
Heavy atoms 36
Fraction sp³ C 0.22
Formula C₂₇H₃₀N₆O₃

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 93.5
  • −1 ≤ LogP ≤ 5 4.45
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 486.6
  • LogP ≤ 5 4.45
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 93.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C=CC(=O)Nc1cc(Nc2nccc(-c3cn(C)c4ccccc34)n2)c(OC)cc1OCCN(C)C
InChI 
InChI=1S/C27H30N6O3/c1-6-26(34)29-22-15-21(24(35-5)16-25(22)36-14-13-32(2)3)31-27-28-12-11-20(30-27)19-17-33(4)23-10-8-7-9-18(19)23/h6-12,15-17H,1,13-14H2,2-5H3,(H,29,34)(H,28,30,31)
InChIKey 
BPMZUKYFIDPLEA-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
YY3
Homolog
P49589

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 28

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)