Ligand profile

1YM

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0AES6 Formula C₁₈H₁₄F₃N₅O₃S
pchembl 8.22 ~6.0 nM
Mol. weight 437.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1YM
UniProt (similar protein)
P0AES6
pchembl
8.220 (~6.0 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 437.40 Da
LogP (Crippen) 4.13
H-bond donors 3
H-bond acceptors 6
TPSA 117.10 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 30
Fraction sp³ C 0.17
Formula C₁₈H₁₄F₃N₅O₃S

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 117.1
  • −1 ≤ LogP ≤ 5 4.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 437.4
  • LogP ≤ 5 4.13
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 117.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cc(c(cn1)c2cc(cnc2)C(=O)O)c3nc(cs3)C(F)(F)F
InChI 
InChI=1S/C18H14F3N5O3S/c1-2-23-17(29)26-14-4-11(15-25-13(8-30-15)18(19,20)21)12(7-24-14)9-3-10(16(27)28)6-22-5-9/h3-8H,2H2,1H3,(H,27,28)(H2,23,24,26,29)
InChIKey 
GLNFAHNABSNEAM-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
ChEMBL
Curation
pdb_similarity_tanimoto
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 88

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

Ligand PDB entry

ChEMBL 99

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)