Ligand profile

ZINC2111578

Virtual-screening candidate from ZINC.

Bound to: KP13_00803 — ATP-dependent RNA helicase srmB

Via homolog UniProt Q9BUQ8 Formula C₁₂H₁₆N₂O₄
Tanimoto 0.69
Mol. weight 252.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2111578
UniProt (similar protein)
Q9BUQ8
Tanimoto
0.692
Target protein
KP13_00803

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 252.27 Da
LogP (Crippen) -0.40
H-bond donors 4
H-bond acceptors 4
TPSA 126.64 Ų
Rotatable bonds 6
Aromatic rings 1 / 1
Heavy atoms 18
Fraction sp³ C 0.33
Formula C₁₂H₁₆N₂O₄

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 126.6
  • −1 ≤ LogP ≤ 5 -0.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 252.3
  • LogP ≤ 5 -0.40
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 126.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@H](Cc1ccccc1C[C@@H](N)C(=O)O)C(=O)O
InChI 
InChI=1S/C12H16N2O4/c13-9(11(15)16)5-7-3-1-2-4-8(7)6-10(14)12(17)18/h1-4,9-10H,5-6,13-14H2,(H,15,16)(H,17,18)/t9-,10-/m1/s1
InChIKey 
PKBDZWBCXCQRQC-NXEZZACHSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
PHE
Homolog
Q9BUQ8

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_00803.

PDB 8

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)