Ligand profile

PCX

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

Bound to: KP13_31943 — Asparagine synthetase B glutamine-hydrolyzing

Via homolog PDB 1mc1 UniProt P0DJQ7 Formula C₉H₁₆N₄O₃
Mol. weight 228.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PCX
PDB
1mc1
UniProt (similar protein)
P0DJQ7
Target protein
KP13_31943

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 228.25 Da
LogP (Crippen) -1.06
H-bond donors 4
H-bond acceptors 3
TPSA 119.51 Ų
Rotatable bonds 6
Aromatic rings 0 / 1
Heavy atoms 16
Fraction sp³ C 0.67
Formula C₉H₁₆N₄O₃

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 119.5
  • −1 ≤ LogP ≤ 5 -1.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 228.3
  • LogP ≤ 5 -1.06
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 119.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N1CCC1=O
InChI 
InChI=1S/C9H16N4O3/c10-9(11)12-4-1-2-6(8(15)16)13-5-3-7(13)14/h6H,1-5H2,(H,15,16)(H4,10,11,12)/t6-/m0/s1
InChIKey 
UYADDEKIZFRINK-LURJTMIESA-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
PF00733

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_31943.

PDB 7

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

Ligand PDB entry

ChEMBL 4

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)