Ligand profile

HCT

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

Bound to: KP13_05461 — Periplasmic murein peptide-binding protein

Via homolog PDB 3dp8 UniProt P33590 Formula C₇H₁₀O₆
Mol. weight 190.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HCT
PDB
3dp8
UniProt (similar protein)
P33590
Target protein
KP13_05461

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 190.15 Da
LogP (Crippen) 0.03
H-bond donors 3
H-bond acceptors 3
TPSA 111.90 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.57
Formula C₇H₁₀O₆

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 111.9
  • −1 ≤ LogP ≤ 5 0.03
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 190.2
  • LogP ≤ 5 0.03
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 111.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CC(=O)O)[C@H](CC(=O)O)C(=O)O
InChI 
InChI=1S/C7H10O6/c8-5(9)2-1-4(7(12)13)3-6(10)11/h4H,1-3H2,(H,8,9)(H,10,11)(H,12,13)/t4-/m1/s1
InChIKey 
LOGBRYZYTBQBTB-SCSAIBSYSA-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
PF00496

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_05461.

PDB 20

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)