Ligand profile

N21

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

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

Via homolog PDB 2y67 UniProt P14900 Formula C₂₂H₂₀N₂O₉S₂
Mol. weight 520.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
N21
PDB
2y67
UniProt (similar protein)
P14900
Target protein
VK055_2476

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 520.54 Da
LogP (Crippen) 2.19
H-bond donors 4
H-bond acceptors 8
TPSA 176.17 Ų
Rotatable bonds 11
Aromatic rings 2 / 3
Heavy atoms 35
Fraction sp³ C 0.18
Formula C₂₂H₂₀N₂O₉S₂

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 176.2
  • −1 ≤ LogP ≤ 5 2.19
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 520.5
  • LogP ≤ 5 2.19
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 176.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1COc2ccc(cc2)\C=C/3\C(=O)NC(=O)S3)S(=O)(=O)N[C@H](CCC(=O)O)C(=O)O
InChI 
InChI=1S/C22H20N2O9S2/c25-19(26)10-9-17(21(28)29)24-35(31,32)16-7-3-14(4-8-16)12-33-15-5-1-13(2-6-15)11-18-20(27)23-22(30)34-18/h1-8,11,17,24H,9-10,12H2,(H,25,26)(H,28,29)(H,23,27,30)/b18-11-/t17-/m1/s1
InChIKey 
BZCXCLVFYJNKLW-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)