Ligand profile

RLI

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 4duh UniProt P0AES6 Formula C₁₇H₁₆N₄O₃S₂
Mol. weight 388.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RLI
PDB
4duh
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 388.47 Da
LogP (Crippen) 4.37
H-bond donors 3
H-bond acceptors 7
TPSA 104.21 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.18
Formula C₁₇H₁₆N₄O₃S₂

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 104.2
  • −1 ≤ LogP ≤ 5 4.37
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 388.5
  • LogP ≤ 5 4.37
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 104.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCC(=O)Nc1nc(c(s1)c2csc(n2)Nc3ccc(cc3)C(=O)O)C
InChI 
InChI=1S/C17H16N4O3S2/c1-3-13(22)21-17-18-9(2)14(26-17)12-8-25-16(20-12)19-11-6-4-10(5-7-11)15(23)24/h4-8H,3H2,1-2H3,(H,19,20)(H,23,24)(H,18,21,22)
InChIKey 
JOAXMWDTALNZFE-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF02518

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_00051.

PDB 87

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

Ligand PDB entry

ChEMBL 100

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)