Ligand profile

CHEMBL573352

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt P24928 Formula C₁₁H₁₃N₃O₅
Mol. weight 267.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL573352
UniProt (similar protein)
P24928
Target protein
KP13_01361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 267.24 Da
LogP (Crippen) -2.56
H-bond donors 4
H-bond acceptors 8
TPSA 130.83 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 19
Fraction sp³ C 0.45
Formula C₁₁H₁₃N₃O₅

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 130.8
  • −1 ≤ LogP ≤ 5 -2.56
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 267.2
  • LogP ≤ 5 -2.56
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 130.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C#C[C@@]1(O)[C@@H](CO)O[C@@H](n2ccc(N)nc2=O)[C@@H]1O
InChI 
InChI=1S/C11H13N3O5/c1-2-11(18)6(5-15)19-9(8(11)16)14-4-3-7(12)13-10(14)17/h1,3-4,6,8-9,15-16,18H,5H2,(H2,12,13,17)/t6-,8+,9-,11-/m1/s1
InChIKey 
JFIWEPHGRUDAJN-DYUFWOLASA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Mechanism
DNA-directed RNA polymerase II subunit RPB1 inhibitor
Curation
pdb_similarity_tanimoto
Binding sites
PF00623' 'PF04998' 'PF05000

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 35

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

Ligand PDB entry

ChEMBL 1

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)