Binder profile

H3M

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

Bound to: PA0480 — 3-oxoadipate enol-lactonase

Via homolog PDB 6brt UniProt A0A0D9Z3K8 C5H6O3
Mol. weight 114.10 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
H3M
PDB
6brt
UniProt (similar protein)
A0A0D9Z3K8
Target protein
PA0480

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 114.10 Da
LogP (Crippen) -0.19
H-bond donors 1
H-bond acceptors 3
TPSA 46.53 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 8
Fraction sp³ C 0.40
Formula C5H6O3

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 114.1
  • LogP ≤ 5 -0.19
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 46.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=C[C@@H](OC1=O)O
InChI 
InChI=1S/C5H6O3/c1-3-2-4(6)8-5(3)7/h2,4,6H,1H3/t4-/m1/s1
InChIKey 
HQIZYPQNJWENRT-SCSAIBSYSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF12697

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA0480.

PDB 13

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)