Ligand profile

GBC

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

Bound to: KP13_02854 — Putrescine aminotransferase

Via homolog PDB 1gbn UniProt P04181 Formula C₇H₁₁NO₂
Mol. weight 141.17 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GBC
PDB
1gbn
UniProt (similar protein)
P04181
Target protein
KP13_02854

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 141.17 Da
LogP (Crippen) 0.51
H-bond donors 2
H-bond acceptors 2
TPSA 63.32 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 10
Fraction sp³ C 0.57
Formula C₇H₁₁NO₂

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 63.3
  • −1 ≤ LogP ≤ 5 0.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 141.2
  • LogP ≤ 5 0.51
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 63.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CC(C=C(C1)C(=O)O)N
InChI 
InChI=1S/C7H11NO2/c8-6-3-1-2-5(4-6)7(9)10/h4,6H,1-3,8H2,(H,9,10)
InChIKey 
ZCGFCFMGAXXBTD-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)