Ligand profile

B39

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

Bound to: KP13_02344 — moeB family protein

Via homolog PDB 5l6i UniProt P22515 Formula C₂₁H₂₅N₅O₄S
Mol. weight 443.53 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B39
PDB
5l6i
UniProt (similar protein)
P22515
Target protein
KP13_02344

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 443.53 Da
LogP (Crippen) 2.06
H-bond donors 3
H-bond acceptors 8
TPSA 132.36 Ų
Rotatable bonds 6
Aromatic rings 3 / 5
Heavy atoms 31
Fraction sp³ C 0.43
Formula C₂₁H₂₅N₅O₄S

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 132.4
  • −1 ≤ LogP ≤ 5 2.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 443.5
  • LogP ≤ 5 2.06
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 132.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)CC[C@@H]2Nc3c4ccn(c4ncn3)[C@@H]5C[C@H]([C@H](C5)O)COS(=O)(=O)N
InChI 
InChI=1S/C21H25N5O4S/c22-31(28,29)30-11-14-9-15(10-19(14)27)26-8-7-17-20(23-12-24-21(17)26)25-18-6-5-13-3-1-2-4-16(13)18/h1-4,7-8,12,14-15,18-19,27H,5-6,9-11H2,(H2,22,28,29)(H,23,24,25)/t14-,15+,18-,19-/m0/s1
InChIKey 
MPUQHZXIXSTTDU-QXGSTGNESA-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
PF00899

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_02344.

PDB 9

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

Ligand PDB entry

ChEMBL 31

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)