Ligand profile

Z25

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

Bound to: KP13_03124 — Dihydropteroate synthase type-1

Via homolog PDB 4db7 UniProt Q81VW8 Formula C₉H₉N₅O₄
Mol. weight 251.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Z25
PDB
4db7
UniProt (similar protein)
Q81VW8
Target protein
KP13_03124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 251.20 Da
LogP (Crippen) -1.39
H-bond donors 4
H-bond acceptors 6
TPSA 154.82 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 18
Fraction sp³ C 0.22
Formula C₉H₉N₅O₄

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 154.8
  • −1 ≤ LogP ≤ 5 -1.39
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 251.2
  • LogP ≤ 5 -1.39
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 154.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CC(=O)O)C1=NNC2=C(C1=O)C(=O)NC(=N2)N
InChI 
InChI=1S/C9H9N5O4/c10-9-11-7-5(8(18)12-9)6(17)3(13-14-7)1-2-4(15)16/h1-2H2,(H,15,16)(H4,10,11,12,14,17,18)
InChIKey 
CGUTUVAIFLDCOT-UHFFFAOYSA-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
PF00809

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_03124.

PDB 46

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

Ligand PDB entry

ChEMBL 26

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)