Ligand profile

FZK

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

Bound to: KP13_04211 — Seryl-tRNA synthetase

Via homolog PDB 6hi0 UniProt A6T6Z0 Formula C₁₂H₁₈N₄O₁₀S
Mol. weight 410.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FZK
PDB
6hi0
UniProt (similar protein)
A6T6Z0
Target protein
KP13_04211

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 410.36 Da
LogP (Crippen) -5.15
H-bond donors 6
H-bond acceptors 12
TPSA 223.27 Ų
Rotatable bonds 7
Aromatic rings 1 / 2
Heavy atoms 27
Fraction sp³ C 0.58
Formula C₁₂H₁₈N₄O₁₀S

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 223.3
  • −1 ≤ LogP ≤ 5 -5.15
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 410.4
  • LogP ≤ 5 -5.15
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 223.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COS(=O)(=O)NC(=O)[C@H](CO)N)O)O
InChI 
InChI=1S/C12H18N4O10S/c13-5(3-17)10(21)15-27(23,24)25-4-6-8(19)9(20)11(26-6)16-2-1-7(18)14-12(16)22/h1-2,5-6,8-9,11,17,19-20H,3-4,13H2,(H,15,21)(H,14,18,22)/t5-,6+,8+,9+,11+/m0/s1
InChIKey 
QIOFKSOPWDKKDG-DANLAGSESA-N

Provenance

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

Method
LigQ sequence
Source
PDB
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 3

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

Ligand PDB entry

ChEMBL 4

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)