Ligand profile

G3H

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

Bound to: VK055_2594 — deoxyribose-phosphate aldolase

Via homolog PDB 6z9i UniProt P0A6L0 Formula C₃H₇O₆P
Mol. weight 170.06 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
G3H
PDB
6z9i
UniProt (similar protein)
P0A6L0
Target protein
VK055_2594

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 170.06 Da
LogP (Crippen) -1.34
H-bond donors 3
H-bond acceptors 4
TPSA 104.06 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 0.67
Formula C₃H₇O₆P

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 104.1
  • −1 ≤ LogP ≤ 5 -1.34
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 170.1
  • LogP ≤ 5 -1.34
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 104.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H](C=O)O)OP(=O)(O)O
InChI 
InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h1,3,5H,2H2,(H2,6,7,8)/t3-/m0/s1
InChIKey 
LXJXRIRHZLFYRP-VKHMYHEASA-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
PF01791

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_2594.

PDB 2

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)