Ligand profile

NSK

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

Bound to: KP13_05459 — L-Ala-D/L-Glu epimerase

Via homolog PDB 2p8b UniProt Q81IL5 Formula C₁₀H₁₈N₂O₅
Mol. weight 246.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NSK
PDB
2p8b
UniProt (similar protein)
Q81IL5
Target protein
KP13_05459

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 246.26 Da
LogP (Crippen) -0.45
H-bond donors 4
H-bond acceptors 4
TPSA 129.72 Ų
Rotatable bonds 9
Aromatic rings 0 / 0
Heavy atoms 17
Fraction sp³ C 0.70
Formula C₁₀H₁₈N₂O₅

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 129.7
  • −1 ≤ LogP ≤ 5 -0.45
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 246.3
  • LogP ≤ 5 -0.45
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 129.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCN)C[C@@H](C(=O)O)NC(=O)CCC(=O)O
InChI 
InChI=1S/C10H18N2O5/c11-6-2-1-3-7(10(16)17)12-8(13)4-5-9(14)15/h7H,1-6,11H2,(H,12,13)(H,14,15)(H,16,17)/t7-/m0/s1
InChIKey 
XEOGRHZGJFTETQ-ZETCQYMHSA-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
PF02746' 'PF13378

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_05459.

PDB 3

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)