Ligand profile

DGZ

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

Bound to: VK055_2794 — pepA Transcriptional Repressor, Aminopeptidase A/I

Via homolog PDB 3t8w UniProt Q8IL11 Formula C₅₇H₆₇N₇O₁₀
Mol. weight 1010.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DGZ
PDB
3t8w
UniProt (similar protein)
Q8IL11
Target protein
VK055_2794

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1010.20 Da
LogP (Crippen) 2.97
H-bond donors 8
H-bond acceptors 11
TPSA 270.37 Ų
Rotatable bonds 32
Aromatic rings 5 / 5
Heavy atoms 74
Fraction sp³ C 0.35
Formula C₅₇H₆₇N₇O₁₀

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 270.4
  • −1 ≤ LogP ≤ 5 2.97
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1010.2
  • LogP ≤ 5 2.97
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 32
  • TPSA ≤ 140 Ų 270.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C#CCCCC(=O)NCCCCC(C(=O)N)NC(=O)C(Cc1ccc(cc1)C(=O)c2ccccc2)NC(=O)COCCOCCNC(=O)C(Cc3ccc4ccccc4c3)NC(=O)C(C(Cc5ccccc5)N)O
InChI 
InChI=1S/C57H67N7O10/c1-2-3-6-22-50(65)60-29-14-13-21-47(54(59)69)63-56(71)49(36-40-23-27-44(28-24-40)52(67)43-18-9-5-10-19-43)62-51(66)38-74-33-32-73-31-30-61-55(70)48(37-41-25-26-42-17-11-12-20-45(42)34-41)64-57(72)53(68)46(58)35-39-15-7-4-8-16-39/h1,4-5,7-12,15-20,23-28,34,46-49,53,68H,3,6,13-14,21-22,29-33,35-38,58H2,(H2,59,69)(H,60,65)(H,61,70)(H,62,66)(H,63,71)(H,64,72)
InChIKey 
DTRONJOHRJXFLK-UHFFFAOYSA-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
PF00883

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_2794.

PDB 9

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

Ligand PDB entry

ChEMBL 100

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)