Ligand profile

87C

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

Bound to: KP13_01784 — Prolyl-tRNA synthetase

Via homolog PDB 5xik UniProt S8G8I1 Formula C₁₆H₂₃N₃O₃
Mol. weight 305.38 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
87C
PDB
5xik
UniProt (similar protein)
S8G8I1
Target protein
KP13_01784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 305.38 Da
LogP (Crippen) 0.19
H-bond donors 2
H-bond acceptors 6
TPSA 84.22 Ų
Rotatable bonds 4
Aromatic rings 1 / 3
Heavy atoms 22
Fraction sp³ C 0.69
Formula C₁₆H₂₃N₃O₃

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 84.2
  • −1 ≤ LogP ≤ 5 0.19
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 305.4
  • LogP ≤ 5 0.19
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 84.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CCC2=C(C1)C(=O)N(C=N2)CC(=O)C[C@@H]3[C@@H](CCCN3)O
InChI 
InChI=1S/C16H23N3O3/c20-11(8-14-15(21)6-3-7-17-14)9-19-10-18-13-5-2-1-4-12(13)16(19)22/h10,14-15,17,21H,1-9H2/t14-,15-/m1/s1
InChIKey 
ZMMDIKHKFCGQDK-HUUCEWRRSA-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
PF00587

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_01784.

PDB 9

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

Ligand PDB entry

ChEMBL 21

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)