Ligand profile

UYD

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

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

Via homolog PDB 6x9n UniProt Q9HW02 Formula C₂₁H₂₆N₈O
Mol. weight 406.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
UYD
PDB
6x9n
UniProt (similar protein)
Q9HW02
Target protein
VK055_2476

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 406.49 Da
LogP (Crippen) 3.27
H-bond donors 4
H-bond acceptors 8
TPSA 116.57 Ų
Rotatable bonds 6
Aromatic rings 4 / 4
Heavy atoms 30
Fraction sp³ C 0.33
Formula C₂₁H₂₆N₈O

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 116.6
  • −1 ≤ LogP ≤ 5 3.27
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 406.5
  • LogP ≤ 5 3.27
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 116.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)c1cc(nn1C)Nc2c3cn[nH]c3nc(n2)N[C@@H](CO)c4ccccc4
InChI 
InChI=1S/C21H26N8O/c1-21(2,3)16-10-17(28-29(16)4)24-18-14-11-22-27-19(14)26-20(25-18)23-15(12-30)13-8-6-5-7-9-13/h5-11,15,30H,12H2,1-4H3,(H3,22,23,24,25,26,27,28)/t15-/m0/s1
InChIKey 
MOLGZLFXZJMRCB-HNNXBMFYSA-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
PF08245

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)