Ligand profile

YH5

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

Bound to: KP13_03124 — Dihydropteroate synthase type-1

Via homolog PDB 5u13 UniProt P0AC13 Formula C₁₄H₁₃N₅O₃S
Mol. weight 331.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
YH5
PDB
5u13
UniProt (similar protein)
P0AC13
Target protein
KP13_03124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 331.36 Da
LogP (Crippen) 1.21
H-bond donors 3
H-bond acceptors 7
TPSA 126.75 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 23
Fraction sp³ C 0.14
Formula C₁₄H₁₃N₅O₃S

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 126.8
  • −1 ≤ LogP ≤ 5 1.21
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 331.4
  • LogP ≤ 5 1.21
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 126.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(cc1)C(=O)CSc2[nH]c3c(n2)C(=O)NC(=N3)N
InChI 
InChI=1S/C14H13N5O3S/c1-22-8-4-2-7(3-5-8)9(20)6-23-14-16-10-11(18-14)17-13(15)19-12(10)21/h2-5H,6H2,1H3,(H4,15,16,17,18,19,21)
InChIKey 
SQNJCPSJSYBCFC-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)