Ligand profile

HGD

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

Bound to: VK055_5124 — ABC transporter family protein

Via homolog PDB 4mrv UniProt Q2G506 Formula C₂₀H₃₂HgN₆O₁₂S₂
Mol. weight 813.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HGD
PDB
4mrv
UniProt (similar protein)
Q2G506
Target protein
VK055_5124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 813.23 Da
LogP (Crippen) -3.88
H-bond donors 10
H-bond acceptors 12
TPSA 317.64 Ų
Rotatable bonds 22
Aromatic rings 0 / 0
Heavy atoms 41
Fraction sp³ C 0.60
Formula C₂₀H₃₂HgN₆O₁₂S₂

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 317.6
  • −1 ≤ LogP ≤ 5 -3.88
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 813.2
  • LogP ≤ 5 -3.88
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 22
  • TPSA ≤ 140 Ų 317.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CC(=O)N[C@@H](CS[Hg]SC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(=O)O)N)C(=O)NCC(=O)O)[C@@H](C(=O)O)N
InChI 
InChI=1S/2C10H17N3O6S.Hg/c2*11-5(10(18)19)1-2-7(14)13-6(4-20)9(17)12-3-8(15)16;/h2*5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19);/q;;+2/p-2/t2*5-,6-;/m00./s1
InChIKey 
LUQCMRZJGIPGCC-PRKWKTPOSA-L

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
PF00664

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_5124.

PDB 7

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)