Ligand profile

NE6

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

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

Via homolog PDB 3dxj UniProt Q8RQE8 Formula C₂₃H₃₁NO₆
Mol. weight 417.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NE6
PDB
3dxj
UniProt (similar protein)
Q8RQE8
Target protein
KP13_01361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 417.50 Da
LogP (Crippen) 4.52
H-bond donors 0
H-bond acceptors 6
TPSA 99.10 Ų
Rotatable bonds 10
Aromatic rings 0 / 1
Heavy atoms 30
Fraction sp³ C 0.52
Formula C₂₃H₃₁NO₆

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 99.1
  • −1 ≤ LogP ≤ 5 4.52
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 417.5
  • LogP ≤ 5 4.52
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 99.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCC/C(=C/C=C(\C)/C(=O)C1C(=O)C=C(OC1=O)[C@H](C)CCC\C=N\C(=O)OC)/C
InChI 
InChI=1S/C23H31NO6/c1-6-9-15(2)11-12-17(4)21(26)20-18(25)14-19(30-22(20)27)16(3)10-7-8-13-24-23(28)29-5/h11-14,16,20H,6-10H2,1-5H3/b15-11+,17-12+,24-13+/t16-,20?/m1/s1
InChIKey 
LTDLIPXLSBMTFP-FSAISGGASA-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
PF00623' 'PF04560' 'PF04997' 'PF04998

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)