Binder profile

SKM

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

Bound to: PA2334 — transcriptional regulator

Via homolog PDB 5ted UniProt Q8Y9N7 C7H10O5
Mol. weight 174.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SKM
PDB
5ted
UniProt (similar protein)
Q8Y9N7
Target protein
PA2334

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 174.15 Da
LogP (Crippen) -1.52
H-bond donors 4
H-bond acceptors 4
TPSA 97.99 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 12
Fraction sp³ C 0.57
Formula C7H10O5

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 174.2
  • LogP ≤ 5 -1.52
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 98.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)O)O)O
InChI 
InChI=1S/C7H10O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,4-6,8-10H,2H2,(H,11,12)/t4-,5-,6-/m1/s1
InChIKey 
JXOHGGNKMLTUBP-HSUXUTPPSA-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
PF03466

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA2334.

PDB 7

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)