Ligand profile

GMZ

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

Bound to: VK055_4017 — bifunctional protein RfaE, domain I

Via homolog PDB 4e84 UniProt B4EB35 Formula C₇H₁₆O₁₃P₂
Mol. weight 370.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GMZ
PDB
4e84
UniProt (similar protein)
B4EB35
Target protein
VK055_4017

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 370.14 Da
LogP (Crippen) -3.63
H-bond donors 8
H-bond acceptors 9
TPSA 223.67 Ų
Rotatable bonds 6
Aromatic rings 0 / 1
Heavy atoms 22
Fraction sp³ C 1.00
Formula C₇H₁₆O₁₃P₂

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 223.7
  • −1 ≤ LogP ≤ 5 -3.63
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 370.1
  • LogP ≤ 5 -3.63
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 223.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)OP(=O)(O)O)O)O)O)O)OP(=O)(O)O
InChI 
InChI=1S/C7H16O13P2/c8-2(1-18-21(12,13)14)6-4(10)3(9)5(11)7(19-6)20-22(15,16)17/h2-11H,1H2,(H2,12,13,14)(H2,15,16,17)/t2-,3+,4+,5+,6-,7+/m1/s1
InChIKey 
LMTGTTLGDUACSJ-QTNLNCNHSA-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
PF00294

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_4017.

PDB 9

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

Ligand PDB entry

ChEMBL 2

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)