Ligand profile

4H4

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

Bound to: KP13_02423 — tRNA (guanine-N(1)-)-methyltransferase

Via homolog PDB 4yql UniProt P43912 Formula C₁₂H₁₃N₅O₄S
Mol. weight 323.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4H4
PDB
4yql
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 323.33 Da
LogP (Crippen) -0.41
H-bond donors 3
H-bond acceptors 7
TPSA 154.20 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 22
Fraction sp³ C 0.25
Formula C₁₂H₁₃N₅O₄S

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 154.2
  • −1 ≤ LogP ≤ 5 -0.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 323.3
  • LogP ≤ 5 -0.41
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 154.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1[C@H]2C[C@@H]2NC(=O)c3c(non3)N)S(=O)(=O)N
InChI 
InChI=1S/C12H13N5O4S/c13-11-10(16-21-17-11)12(18)15-9-5-8(9)6-1-3-7(4-2-6)22(14,19)20/h1-4,8-9H,5H2,(H2,13,17)(H,15,18)(H2,14,19,20)/t8-,9+/m1/s1
InChIKey 
ZXELRJOXFOOICP-BDAKNGLRSA-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
PF01746

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_02423.

PDB 88

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

Ligand PDB entry

ChEMBL 38

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)