Ligand profile

051

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

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

Via homolog PDB 2xpc UniProt P14900 Formula C₂₆H₂₃FN₂O₇S
Mol. weight 526.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
051
PDB
2xpc
UniProt (similar protein)
P14900
Target protein
VK055_2476

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 526.54 Da
LogP (Crippen) 3.66
H-bond donors 3
H-bond acceptors 6
TPSA 153.79 Ų
Rotatable bonds 8
Aromatic rings 3 / 4
Heavy atoms 37
Fraction sp³ C 0.27
Formula C₂₆H₂₃FN₂O₇S

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 3.66
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 526.5
  • LogP ≤ 5 3.66
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • 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)NC4CCC(CC4C(=O)O)C(=O)O
InChI 
InChI=1S/C26H23FN2O7S/c27-23-9-15(13-28)1-2-19(23)14-36-20-6-3-17-11-21(7-4-16(17)10-20)37(34,35)29-24-8-5-18(25(30)31)12-22(24)26(32)33/h1-4,6-7,9-11,18,22,24,29H,5,8,12,14H2,(H,30,31)(H,32,33)
InChIKey 
NYXJFBFDAFPUOG-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)