Ligand profile

N04

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

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

Via homolog PDB 2y66 UniProt P14900 Formula C₂₃H₂₀N₂O₈S
Mol. weight 484.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
N04
PDB
2y66
UniProt (similar protein)
P14900
Target protein
VK055_2476

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 484.49 Da
LogP (Crippen) 2.64
H-bond donors 4
H-bond acceptors 7
TPSA 159.10 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 34
Fraction sp³ C 0.17
Formula C₂₃H₂₀N₂O₈S

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 159.1
  • −1 ≤ LogP ≤ 5 2.64
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 484.5
  • LogP ≤ 5 2.64
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 159.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)C(=O)N[C@H](CCC(=O)O)C(=O)O)COc2cccc(c2)\C=C/3\C(=O)NC(=O)S3
InChI 
InChI=1S/C23H20N2O8S/c26-19(27)8-7-17(22(30)31)24-20(28)15-5-1-4-14(9-15)12-33-16-6-2-3-13(10-16)11-18-21(29)25-23(32)34-18/h1-6,9-11,17H,7-8,12H2,(H,24,28)(H,26,27)(H,30,31)(H,25,29,32)/b18-11-/t17-/m1/s1
InChIKey 
LTRBYYDVMAAOIG-LVSMMTLPSA-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)