Ligand profile

GCS

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

Bound to: KP13_00473 — Biofilm PGA synthesis lipoprotein pgaB

Via homolog PDB 4p7n UniProt P75906 Formula C₆H₁₃NO₅
Mol. weight 179.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GCS
PDB
4p7n
UniProt (similar protein)
P75906
Target protein
KP13_00473

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 179.17 Da
LogP (Crippen) -3.25
H-bond donors 5
H-bond acceptors 6
TPSA 116.17 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 12
Fraction sp³ C 1.00
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 116.2
  • −1 ≤ LogP ≤ 5 -3.25
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 179.2
  • LogP ≤ 5 -3.25
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 116.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)N)O)O)O
InChI 
InChI=1S/C6H13NO5/c7-3-5(10)4(9)2(1-8)12-6(3)11/h2-6,8-11H,1,7H2/t2-,3-,4-,5-,6-/m1/s1
InChIKey 
MSWZFWKMSRAUBD-QZABAPFNSA-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
PF14883

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_00473.

ZINC 50

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

Compound Similarity (Tanimoto)