Ligand profile

HZ2

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 6qe0 UniProt P37634 Formula C₂₆H₃₆N₁₂O₉
Mol. weight 660.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HZ2
PDB
6qe0
UniProt (similar protein)
P37634
Target protein
VK055_3605

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 660.65 Da
LogP (Crippen) -4.00
H-bond donors 9
H-bond acceptors 20
TPSA 311.42 Ų
Rotatable bonds 13
Aromatic rings 4 / 6
Heavy atoms 47
Fraction sp³ C 0.58
Formula C₂₆H₃₆N₁₂O₉

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 -4.00
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 660.6
  • LogP ≤ 5 -4.00
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • 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(CC[C@@H](C(=O)O)N)CCNc4c5c(ncn4)n(cn5)[C@H]6[C@@H]([C@@H]([C@H](O6)CO)O)O)O)O)N
InChI 
InChI=1S/C26H36N12O9/c27-11(26(44)45)1-3-36(5-12-16(40)18(42)24(46-12)37-9-34-14-20(28)30-7-32-22(14)37)4-2-29-21-15-23(33-8-31-21)38(10-35-15)25-19(43)17(41)13(6-39)47-25/h7-13,16-19,24-25,39-43H,1-6,27H2,(H,44,45)(H2,28,30,32)(H,29,31,33)/t11-,12+,13+,16+,17+,18+,19+,24+,25+/m0/s1
InChIKey 
UAGVZMOWWSWEAM-CZUOOHDMSA-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)