Ligand profile

6DF

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

Bound to: KP13_03438 — Aminotransferase class-III family protein

Via homolog PDB 5g09 UniProt A0A1C7D190 Formula C₁₆H₁₉N₂O₅P
Mol. weight 350.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6DF
PDB
5g09
UniProt (similar protein)
A0A1C7D190
Target protein
KP13_03438

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 350.31 Da
LogP (Crippen) 2.89
H-bond donors 3
H-bond acceptors 5
TPSA 112.24 Ų
Rotatable bonds 6
Aromatic rings 2 / 2
Heavy atoms 24
Fraction sp³ C 0.25
Formula C₁₆H₁₉N₂O₅P

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 112.2
  • −1 ≤ LogP ≤ 5 2.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 350.3
  • LogP ≤ 5 2.89
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 112.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H](C)c2ccccc2)O
InChI 
InChI=1S/C16H19N2O5P/c1-11(13-6-4-3-5-7-13)18-9-15-14(10-23-24(20,21)22)8-17-12(2)16(15)19/h3-9,11,19H,10H2,1-2H3,(H2,20,21,22)/b18-9+/t11-/m1/s1
InChIKey 
ZBWJIKYNMPWLJE-PBFYJAPKSA-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
PF00202

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_03438.

PDB 3

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

Ligand PDB entry

ZINC 11

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)