Ligand profile

2KT

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

Bound to: VK055_4699 — dihydrodipicolinate synthase

Via homolog PDB 3tdf UniProt D0CFC3 Formula C₄H₆O₃
Mol. weight 102.09 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2KT
PDB
3tdf
UniProt (similar protein)
D0CFC3
Target protein
VK055_4699

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 102.09 Da
LogP (Crippen) 0.05
H-bond donors 1
H-bond acceptors 2
TPSA 54.37 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 7
Fraction sp³ C 0.50
Formula C₄H₆O₃

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 54.4
  • −1 ≤ LogP ≤ 5 0.05
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 102.1
  • LogP ≤ 5 0.05
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 54.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCC(=O)C(=O)O
InChI 
InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7)
InChIKey 
TYEYBOSBBBHJIV-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
PF00701

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4699.

PDB 6

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

Ligand PDB entry

ChEMBL 1

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)