Ligand profile

42U

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

Bound to: KP13_01361 — DNA-directed RNA polymerase subunit beta'

Via homolog PDB 4xsz UniProt A7ZUK2 Formula C₂₂H₂₃F₄N₅
Mol. weight 433.45 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
42U
PDB
4xsz
UniProt (similar protein)
A7ZUK2
Target protein
KP13_01361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 433.45 Da
LogP (Crippen) 4.22
H-bond donors 3
H-bond acceptors 4
TPSA 55.98 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 31
Fraction sp³ C 0.32
Formula C₂₂H₂₃F₄N₅

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 56.0
  • −1 ≤ LogP ≤ 5 4.22
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 433.5
  • LogP ≤ 5 4.22
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 56.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1c2c(c[nH]n2)c3ccc(c(c3)C(F)(F)F)NCCN4CCNCC4)F
InChI 
InChI=1S/C22H23F4N5/c23-17-4-1-15(2-5-17)21-18(14-29-30-21)16-3-6-20(19(13-16)22(24,25)26)28-9-12-31-10-7-27-8-11-31/h1-6,13-14,27-28H,7-12H2,(H,29,30)
InChIKey 
OXSJLZKYOPQBJE-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
PF04561' 'PF04563' 'PF04565' 'PF04998' 'PF05000' 'PF10385

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_01361.

PDB 34

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

Ligand PDB entry

ChEMBL 2

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)