Ligand profile

WZD

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

Bound to: KP13_31828 — UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase

Via homolog PDB 7b6q UniProt P22188 Formula C₁₂H₁₁N₃O
Mol. weight 213.24 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
WZD
PDB
7b6q
UniProt (similar protein)
P22188
Target protein
KP13_31828

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 213.24 Da
LogP (Crippen) 2.77
H-bond donors 2
H-bond acceptors 3
TPSA 53.85 Ų
Rotatable bonds 3
Aromatic rings 3 / 3
Heavy atoms 16
Fraction sp³ C 0.08
Formula C₁₂H₁₁N₃O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 53.9
  • −1 ≤ LogP ≤ 5 2.77
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 213.2
  • LogP ≤ 5 2.77
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 53.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)[nH]c(n2)NCc3ccco3
InChI 
InChI=1S/C12H11N3O/c1-2-6-11-10(5-1)14-12(15-11)13-8-9-4-3-7-16-9/h1-7H,8H2,(H2,13,14,15)
InChIKey 
VVXTVMPZTWGDLF-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
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 KP13_31828.

PDB 17

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 9

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)