Ligand profile

D5F

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

Bound to: KP13_02199 — Lysyl-tRNA synthetase

Via homolog PDB 6kcn UniProt W7JP72 Formula C₁₇H₂₀O₄
Mol. weight 288.34 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D5F
PDB
6kcn
UniProt (similar protein)
W7JP72
Target protein
KP13_02199

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 288.34 Da
LogP (Crippen) 3.57
H-bond donors 2
H-bond acceptors 4
TPSA 70.67 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 21
Fraction sp³ C 0.47
Formula C₁₇H₂₀O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 70.7
  • −1 ≤ LogP ≤ 5 3.57
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 288.3
  • LogP ≤ 5 3.57
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 70.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1CCC[C@@H](C1)CC2=Cc3cc(cc(c3C(=O)O2)O)O
InChI 
InChI=1S/C17H20O4/c1-10-3-2-4-11(5-10)6-14-8-12-7-13(18)9-15(19)16(12)17(20)21-14/h7-11,18-19H,2-6H2,1H3/t10-,11-/m0/s1
InChIKey 
JSPLICPLSKXJBM-QWRGUYRKSA-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)