Ligand profile

LKM

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

Bound to: VK055_2476 — UDP-N-acetylmuramate--alanine ligase

Via homolog PDB 2vtd UniProt P14900 Formula C₂₃H₁₉FN₂O₇S
Mol. weight 486.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LKM
PDB
2vtd
UniProt (similar protein)
P14900
Target protein
VK055_2476

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 486.48 Da
LogP (Crippen) 3.03
H-bond donors 3
H-bond acceptors 6
TPSA 153.79 Ų
Rotatable bonds 10
Aromatic rings 3 / 3
Heavy atoms 34
Fraction sp³ C 0.17
Formula C₂₃H₁₉FN₂O₇S

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 153.8
  • −1 ≤ LogP ≤ 5 3.03
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 486.5
  • LogP ≤ 5 3.03
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 153.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(cc1C#N)F)COc2ccc3cc(ccc3c2)S(=O)(=O)NC(CCC(=O)O)C(=O)O
InChI 
InChI=1S/C23H19FN2O7S/c24-20-9-14(12-25)1-2-17(20)13-33-18-5-3-16-11-19(6-4-15(16)10-18)34(31,32)26-21(23(29)30)7-8-22(27)28/h1-6,9-11,21,26H,7-8,13H2,(H,27,28)(H,29,30)
InChIKey 
IRJUSGUHNFMVCK-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
PF02875' 'PF08245' 'PF21799

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_2476.

PDB 17

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)