Ligand profile

NVD

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

Bound to: KP13_00203 — putative 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase

Via homolog PDB 5qr8 UniProt P22557 Formula C₁₁H₁₅N₅
Mol. weight 217.28 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
NVD
PDB
5qr8
UniProt (similar protein)
P22557
Target protein
KP13_00203

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 217.28 Da
LogP (Crippen) 1.09
H-bond donors 1
H-bond acceptors 5
TPSA 45.98 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 16
Fraction sp³ C 0.27
Formula C₁₁H₁₅N₅

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 46.0
  • −1 ≤ LogP ≤ 5 1.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 217.3
  • LogP ≤ 5 1.09
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 46.0
PAINS Alert

Matches PAINS filter: anil_di_alk_E(186). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)c1ccc(cc1)CNn2cnnc2
InChI 
InChI=1S/C11H15N5/c1-15(2)11-5-3-10(4-6-11)7-14-16-8-12-13-9-16/h3-6,8-9,14H,7H2,1-2H3
InChIKey 
ZPORTAACPUBAHX-UHFFFAOYSA-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
PF00155

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_00203.

PDB 32

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

Ligand PDB entry

ChEMBL 1

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)