Ligand profile

VLS

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

Bound to: KP13_02854 — Putrescine aminotransferase

Via homolog PDB 7jx9 UniProt P04181 Formula C₆H₁₃NO₅
Mol. weight 179.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VLS
PDB
7jx9
UniProt (similar protein)
P04181
Target protein
KP13_02854

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 179.17 Da
LogP (Crippen) -2.62
H-bond donors 5
H-bond acceptors 5
TPSA 110.02 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.83
Formula C₆H₁₃NO₅

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 110.0
  • −1 ≤ LogP ≤ 5 -2.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 179.2
  • LogP ≤ 5 -2.62
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 110.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(=O)O)NC(CO)(CO)CO
InChI 
InChI=1S/C6H13NO5/c8-2-6(3-9,4-10)7-1-5(11)12/h7-10H,1-4H2,(H,11,12)
InChIKey 
SEQKRHFRPICQDD-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
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_02854.

PDB 12

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)