Ligand profile

CHEMBL4467050

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_04211 — Seryl-tRNA synthetase

Via homolog UniProt P95689 Formula C₁₃H₁₈IN₇O₈S
pchembl 6.42 ~380.2 nM
Mol. weight 559.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4467050
UniProt (similar protein)
P95689
pchembl
6.420 (~380.2 nM)
Target protein
KP13_04211

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 559.30 Da
LogP (Crippen) -3.67
H-bond donors 6
H-bond acceptors 14
TPSA 238.03 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 30
Fraction sp³ C 0.54
Formula C₁₃H₁₈IN₇O₈S

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 238.0
  • −1 ≤ LogP ≤ 5 -3.67
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 559.3
  • LogP ≤ 5 -3.67
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 238.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc(I)nc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)NC(=O)[C@@H](N)CO)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C13H18IN7O8S/c14-13-18-9(16)6-10(19-13)21(3-17-6)12-8(24)7(23)5(29-12)2-28-30(26,27)20-11(25)4(15)1-22/h3-5,7-8,12,22-24H,1-2,15H2,(H,20,25)(H2,16,18,19)/t4-,5+,7+,8+,12+/m0/s1
InChIKey 
DGNJFKKZVYPDMV-IZKXYQSCSA-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
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 KP13_04211.

PDB 4

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

Ligand PDB entry

ChEMBL 3

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)