Ligand profile

13N

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

Bound to: VK055_2094 — htpG

Via homolog PDB 2xx5 UniProt P02829 Formula C₂₅H₂₇ClN₂O₅
Mol. weight 470.95 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
13N
PDB
2xx5
UniProt (similar protein)
P02829
Target protein
VK055_2094

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 470.95 Da
LogP (Crippen) 3.66
H-bond donors 4
H-bond acceptors 5
TPSA 115.73 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 33
Fraction sp³ C 0.32
Formula C₂₅H₂₇ClN₂O₅

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 115.7
  • −1 ≤ LogP ≤ 5 3.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 471.0
  • LogP ≤ 5 3.66
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 115.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)CNC(=O)[C@@H]2CCC\C=C\CCNC(=O)c3c(cc(c(c3CC2=O)Cl)O)O
InChI 
InChI=1S/C25H27ClN2O5/c26-23-18-13-19(29)17(24(32)28-15-16-9-5-4-6-10-16)11-7-2-1-3-8-12-27-25(33)22(18)20(30)14-21(23)31/h1,3-6,9-10,14,17,30-31H,2,7-8,11-13,15H2,(H,27,33)(H,28,32)/b3-1+/t17-/m1/s1
InChIKey 
POTAVWZRFSZHOW-XKKXFUJGSA-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
PF02518

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2094.

PDB 27

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

Ligand PDB entry

ChEMBL 6

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)