Ligand profile

UXP

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

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

Via homolog PDB 6x9f UniProt Q9HW02 Formula C₁₇H₂₂N₈O
Mol. weight 354.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
UXP
PDB
6x9f
UniProt (similar protein)
Q9HW02
Target protein
VK055_2476

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 354.42 Da
LogP (Crippen) 2.05
H-bond donors 4
H-bond acceptors 7
TPSA 118.64 Ų
Rotatable bonds 5
Aromatic rings 3 / 5
Heavy atoms 26
Fraction sp³ C 0.53
Formula C₁₇H₂₂N₈O

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 118.6
  • −1 ≤ LogP ≤ 5 2.05
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 354.4
  • LogP ≤ 5 2.05
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 118.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c([nH]nc1Nc2c3c[nH]nc3nc(n2)N4CCCC[C@@H]4CO)C5CC5
InChI 
InChI=1S/C17H22N8O/c26-9-11-3-1-2-6-25(11)17-20-15(12-8-18-24-16(12)21-17)19-14-7-13(22-23-14)10-4-5-10/h7-8,10-11,26H,1-6,9H2,(H3,18,19,20,21,22,23,24)/t11-/m1/s1
InChIKey 
YKDFQYJWKSLGGG-LLVKDONJSA-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)