Ligand profile

5ND

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

Bound to: KP13_05435 — putative permease

Via homolog PDB 4d1d UniProt D6R8X8 Formula C₁₄H₁₂N₂O₂
Mol. weight 240.26 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5ND
PDB
4d1d
UniProt (similar protein)
D6R8X8
Target protein
KP13_05435

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 240.26 Da
LogP (Crippen) 1.59
H-bond donors 2
H-bond acceptors 2
TPSA 58.20 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 18
Fraction sp³ C 0.14
Formula C₁₄H₁₂N₂O₂

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 1.59
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 240.3
  • LogP ≤ 5 1.59
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 58.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2cc(ccc2c1)C[C@@H]3C(=O)NC(=O)N3
InChI 
InChI=1S/C14H12N2O2/c17-13-12(15-14(18)16-13)8-9-5-6-10-3-1-2-4-11(10)7-9/h1-7,12H,8H2,(H2,15,16,17,18)/t12-/m1/s1
InChIKey 
CHRJCAZBQNADBP-GFCCVEGCSA-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
PF02133

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_05435.

PDB 4

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)