Ligand profile

AMI

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

Bound to: KP13_05659 — chitinase II

Via homolog PDB 1e6r UniProt Q54276 Formula C₉H₁₆N₂O₄
Mol. weight 216.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AMI
PDB
1e6r
UniProt (similar protein)
Q54276
Target protein
KP13_05659

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 216.24 Da
LogP (Crippen) -1.98
H-bond donors 3
H-bond acceptors 6
TPSA 85.52 Ų
Rotatable bonds 1
Aromatic rings 0 / 2
Heavy atoms 15
Fraction sp³ C 0.89
Formula C₉H₁₆N₂O₄

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 85.5
  • −1 ≤ LogP ≤ 5 -1.98
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 216.2
  • LogP ≤ 5 -1.98
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 85.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)C1=N[C@@H]2[C@H]([C@@H]([C@H]([C@@H]2O1)CO)O)O
InChI 
InChI=1S/C9H16N2O4/c1-11(2)9-10-5-7(14)6(13)4(3-12)8(5)15-9/h4-8,12-14H,3H2,1-2H3/t4-,5-,6-,7-,8+/m1/s1
InChIKey 
MKJAYSJDHSEFRI-PVFLNQBWSA-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
PF00704

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_05659.

PDB 7

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

Ligand PDB entry

ChEMBL 37

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)