Ligand profile

F6O

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_02199 — Lysyl-tRNA synthetase

Via homolog PDB 7bt5 UniProt Q8IDJ8 Formula C₂₉H₄₀N₈O₃S
Mol. weight 580.76 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
F6O
PDB
7bt5
UniProt (similar protein)
Q8IDJ8
Target protein
KP13_02199

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 580.76 Da
LogP (Crippen) 3.77
H-bond donors 2
H-bond acceptors 11
TPSA 115.82 Ų
Rotatable bonds 9
Aromatic rings 3 / 5
Heavy atoms 41
Fraction sp³ C 0.48
Formula C₂₉H₄₀N₈O₃S

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 115.8
  • −1 ≤ LogP ≤ 5 3.77
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 580.8
  • LogP ≤ 5 3.77
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 11
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 115.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)S(=O)(=O)c1ccccc1Nc2ncnc(n2)Nc3ccc(cc3OC)N4CCC(CC4)N5CCN(CC5)C
InChI 
InChI=1S/C29H40N8O3S/c1-21(2)41(38,39)27-8-6-5-7-25(27)33-29-31-20-30-28(34-29)32-24-10-9-23(19-26(24)40-4)36-13-11-22(12-14-36)37-17-15-35(3)16-18-37/h5-10,19-22H,11-18H2,1-4H3,(H2,30,31,32,33,34)
InChIKey 
MGGBYMDAPCCKCT-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
PDB
Binding sites
PF00152

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_02199.

PDB 17

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

Ligand PDB entry

ChEMBL 2

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)