Ligand profile

2NV

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

Bound to: KP13_03672 — Peptidyl-prolyl cis-trans isomerase D

Via homolog PDB 6vj6 UniProt Q81CB1 Formula C₁₃H₂₉NO₅
Mol. weight 279.38 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2NV
PDB
6vj6
UniProt (similar protein)
Q81CB1
Target protein
KP13_03672

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 279.38 Da
LogP (Crippen) 0.44
H-bond donors 1
H-bond acceptors 6
TPSA 72.17 Ų
Rotatable bonds 15
Aromatic rings 0 / 0
Heavy atoms 19
Fraction sp³ C 1.00
Formula C₁₃H₂₉NO₅

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 72.2
  • −1 ≤ LogP ≤ 5 0.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 279.4
  • LogP ≤ 5 0.44
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 72.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCOCCOCCOCCOCCOC[C@@H](C)N
InChI 
InChI=1S/C13H29NO5/c1-3-15-4-5-16-6-7-17-8-9-18-10-11-19-12-13(2)14/h13H,3-12,14H2,1-2H3/t13-/m1/s1
InChIKey 
LPPZTQZWMYYVLK-CYBMUJFWSA-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
PF13616

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_03672.

ZINC 1

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)