Ligand profile

G5A

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

Bound to: VK055_4487 — alanine--tRNA ligase

Via homolog PDB 3hy0 UniProt P00957 Formula C₁₂H₁₇N₇O₇S
Mol. weight 403.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
G5A
PDB
3hy0
UniProt (similar protein)
P00957
Target protein
VK055_4487

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 403.38 Da
LogP (Crippen) -3.64
H-bond donors 5
H-bond acceptors 13
TPSA 217.80 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 27
Fraction sp³ C 0.50
Formula C₁₂H₁₇N₇O₇S

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 -3.64
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 403.4
  • LogP ≤ 5 -3.64
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • 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)CN)O)O)N
InChI 
InChI=1S/C12H17N7O7S/c13-1-6(20)18-27(23,24)25-2-5-8(21)9(22)12(26-5)19-4-17-7-10(14)15-3-16-11(7)19/h3-5,8-9,12,21-22H,1-2,13H2,(H,18,20)(H2,14,15,16)/t5-,8-,9-,12-/m1/s1
InChIKey 
AMWPZASLDLLQFT-JJNLEZRASA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF01411

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4487.

PDB 6

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)