Ligand profile

NVM

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 5qra UniProt P22557 Formula C₁₁H₁₄N₂OS
Mol. weight 222.31 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NVM
PDB
5qra
UniProt (similar protein)
P22557
Target protein
KP13_00203

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 222.31 Da
LogP (Crippen) 2.53
H-bond donors 0
H-bond acceptors 3
TPSA 33.20 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 15
Fraction sp³ C 0.45
Formula C₁₁H₁₄N₂OS

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 33.2
  • −1 ≤ LogP ≤ 5 2.53
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 222.3
  • LogP ≤ 5 2.53
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 33.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1CCN(C=CC1)C(=O)c2cscn2
InChI 
InChI=1S/C11H14N2OS/c1-9-3-2-5-13(6-4-9)11(14)10-7-15-8-12-10/h2,5,7-9H,3-4,6H2,1H3/t9-/m1/s1
InChIKey 
UZPOAAASLKBFBY-SECBINFHSA-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)