Ligand profile

5CA

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

Bound to: KP13_01784 — Prolyl-tRNA synthetase

Via homolog PDB 1nj1 UniProt O26708 Formula C₁₃H₁₉N₇O₇S₂
Mol. weight 449.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5CA
PDB
1nj1
UniProt (similar protein)
O26708
Target protein
KP13_01784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 449.47 Da
LogP (Crippen) -3.34
H-bond donors 6
H-bond acceptors 14
TPSA 217.80 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.54
Formula C₁₃H₁₉N₇O₇S₂

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 217.8
  • −1 ≤ LogP ≤ 5 -3.34
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 449.5
  • LogP ≤ 5 -3.34
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 217.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CS)N)O)O)N
InChI 
InChI=1S/C13H19N7O7S2/c14-5(2-28)12(23)19-29(24,25)26-1-6-8(21)9(22)13(27-6)20-4-18-7-10(15)16-3-17-11(7)20/h3-6,8-9,13,21-22,28H,1-2,14H2,(H,19,23)(H2,15,16,17)/t5-,6+,8+,9+,13+/m0/s1
InChIKey 
FTSDEWPMACCNGN-YTMOPEAISA-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)