Ligand profile

CHEMBL434782

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0059 — arginine--tRNA ligase

Via homolog UniProt P54136 Formula C₁₆H₂₈N₉O₇P
pchembl 8.12 ~7.6 nM
Mol. weight 489.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL434782
UniProt (similar protein)
P54136
pchembl
8.120 (~7.6 nM)
Target protein
VK055_0059

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 489.43 Da
LogP (Crippen) -2.25
H-bond donors 8
H-bond acceptors 13
TPSA 262.99 Ų
Rotatable bonds 11
Aromatic rings 2 / 3
Heavy atoms 33
Fraction sp³ C 0.62
Formula C₁₆H₂₈N₉O₇P

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 263.0
  • −1 ≤ LogP ≤ 5 -2.25
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 489.4
  • LogP ≤ 5 -2.25
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 263.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N=C(N)NCCC[C@H](N)COP(=O)(O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O
InChI 
InChI=1S/C16H28N9O7P/c17-8(2-1-3-21-16(19)20)4-30-33(28,29)31-5-9-11(26)12(27)15(32-9)25-7-24-10-13(18)22-6-23-14(10)25/h6-9,11-12,15,26-27H,1-5,17H2,(H,28,29)(H2,18,22,23)(H4,19,20,21)/t8-,9+,11+,12+,15+/m0/s1
InChIKey 
XYAYHVCXSXJVSY-OPYVMVOTSA-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
Curation
pdb_similarity_tanimoto
Binding sites
PF00750

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_0059.

PDB 2

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

Ligand PDB entry

ChEMBL 1

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)