Ligand profile

88D

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

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

Via homolog PDB 5uhf UniProt P9WGY7 Formula C₂₁H₂₀N₂O₂Se
Mol. weight 411.36 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
88D
PDB
5uhf
UniProt (similar protein)
P9WGY7
Target protein
KP13_01361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 411.36 Da
LogP (Crippen) 3.03
H-bond donors 2
H-bond acceptors 2
TPSA 58.20 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.14
Formula C₂₁H₂₀N₂O₂Se

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 58.2
  • −1 ≤ LogP ≤ 5 3.03
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 411.4
  • LogP ≤ 5 3.03
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 58.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccc[se]3
InChI 
InChI=1S/C21H20N2O2Se/c1-15-8-5-6-11-17(15)22-20(24)18(14-16-9-3-2-4-10-16)23-21(25)19-12-7-13-26-19/h2-13,18H,14H2,1H3,(H,22,24)(H,23,25)/t18-/m1/s1
InChIKey 
AGKDXQQYJWMFAB-GOSISDBHSA-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
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)