Ligand profile

GOM

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

Bound to: KP13_01853 — Glutamyl-Q tRNA(Asp) synthetase

Via homolog PDB 1n78 UniProt P27000 Formula C₁₅H₂₂N₆O₉P⁻
Mol. weight 461.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GOM
PDB
1n78
UniProt (similar protein)
P27000
Target protein
KP13_01853

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 461.35 Da
LogP (Crippen) -4.33
H-bond donors 4
H-bond acceptors 14
TPSA 245.67 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.60
Formula C₁₅H₂₂N₆O₉P⁻

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 245.7
  • −1 ≤ LogP ≤ 5 -4.33
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 461.3
  • LogP ≤ 5 -4.33
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 245.7
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)CO[P@](=O)([O-])OC[C@H](CCC(=O)[O-])[NH3+])O)O)N
InChI 
InChI=1S/C15H23N6O9P/c16-7(1-2-9(22)23)3-28-31(26,27)29-4-8-11(24)12(25)15(30-8)21-6-20-10-13(17)18-5-19-14(10)21/h5-8,11-12,15,24-25H,1-4,16H2,(H,22,23)(H,26,27)(H2,17,18,19)/p-1/t7-,8+,11+,12+,15+/m0/s1
InChIKey 
JDELUWYDJMPPMI-SBZSCLMQSA-M

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
PF00749

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_01853.

PDB 4

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)