Ligand profile

50M

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5cdo UniProt P66937 Formula C₁₇H₁₈N₄O₆
Mol. weight 374.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
50M
PDB
5cdo
UniProt (similar protein)
P66937
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 374.35 Da
LogP (Crippen) 1.33
H-bond donors 2
H-bond acceptors 6
TPSA 134.37 Ų
Rotatable bonds 1
Aromatic rings 1 / 4
Heavy atoms 27
Fraction sp³ C 0.47
Formula C₁₇H₁₈N₄O₆

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 134.4
  • −1 ≤ LogP ≤ 5 1.33
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 374.4
  • LogP ≤ 5 1.33
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 134.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1CN2c3ccc(cc3C[C@]4([C@H]2[C@@H](O1)C)C(=O)NC(=O)N=C4O)[N+](=O)[O-]
InChI 
InChI=1S/C17H18N4O6/c1-8-7-20-12-4-3-11(21(25)26)5-10(12)6-17(13(20)9(2)27-8)14(22)18-16(24)19-15(17)23/h3-5,8-9,13H,6-7H2,1-2H3,(H2,18,19,22,23,24)/t8-,9+,13-/m1/s1
InChIKey 
DJZPHYIXNUOVJU-VYUIOLGVSA-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
PF00521' 'PF01751

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)