Ligand profile

CHEMBL5205862

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0276 — threonine--tRNA ligase

Via homolog UniProt A0A3F3IEK2 Formula C₃₀H₂₈Cl₂F₃N₅O₄
pchembl 6.24 ~575.4 nM
Mol. weight 650.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5205862
UniProt (similar protein)
A0A3F3IEK2
pchembl
6.240 (~575.4 nM)
Target protein
VK055_0276

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 650.49 Da
LogP (Crippen) 4.46
H-bond donors 4
H-bond acceptors 7
TPSA 139.34 Ų
Rotatable bonds 10
Aromatic rings 4 / 4
Heavy atoms 44
Fraction sp³ C 0.27
Formula C₃₀H₂₈Cl₂F₃N₅O₄

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 139.3
  • −1 ≤ LogP ≤ 5 4.46
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 650.5
  • LogP ≤ 5 4.46
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 139.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](O)[C@H](N)C(=O)N[C@@H](CNC(=O)CCn1cnc2cc(Cl)c(Cl)cc2c1=O)c1cccc(-c2ccc(C(F)(F)F)cc2)c1
InChI 
InChI=1S/C30H28Cl2F3N5O4/c1-16(41)27(36)28(43)39-25(19-4-2-3-18(11-19)17-5-7-20(8-6-17)30(33,34)35)14-37-26(42)9-10-40-15-38-24-13-23(32)22(31)12-21(24)29(40)44/h2-8,11-13,15-16,25,27,41H,9-10,14,36H2,1H3,(H,37,42)(H,39,43)/t16-,25+,27+/m1/s1
InChIKey 
MITSAJKYFZWXSM-YDZMPMGISA-N

Provenance

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

Method
LigQ sequence
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00587

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_0276.

PDB 12

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)