Ligand profile

HY8

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

Bound to: VK055_3605 — protein involved in utilization of DNA as a carbon source

Via homolog PDB 6qdx UniProt P37634 Formula C₂₇H₃₈N₁₂O₉
Mol. weight 674.68 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HY8
PDB
6qdx
UniProt (similar protein)
P37634
Target protein
VK055_3605

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 674.68 Da
LogP (Crippen) -3.61
H-bond donors 9
H-bond acceptors 20
TPSA 311.42 Ų
Rotatable bonds 14
Aromatic rings 4 / 6
Heavy atoms 48
Fraction sp³ C 0.59
Formula C₂₇H₃₈N₁₂O₉

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 311.4
  • −1 ≤ LogP ≤ 5 -3.61
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 674.7
  • LogP ≤ 5 -3.61
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 311.4
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)CN(CCCNc4c5c(ncn4)n(cn5)[C@@H]6[C@@H]([C@@H]([C@@H](O6)CO)O)O)CC[C@@H](C(=O)O)N)O)O)N
InChI 
InChI=1S/C27H38N12O9/c28-12(27(45)46)2-5-37(6-13-17(41)19(43)25(47-13)38-10-35-15-21(29)31-8-33-23(15)38)4-1-3-30-22-16-24(34-9-32-22)39(11-36-16)26-20(44)18(42)14(7-40)48-26/h8-14,17-20,25-26,40-44H,1-7,28H2,(H,45,46)(H2,29,31,33)(H,30,32,34)/t12-,13-,14-,17+,18+,19+,20+,25+,26-/m0/s1
InChIKey 
BNMNWGQODJWABC-JIDNCIPASA-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
PF04378

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_3605.

PDB 1

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)