Ligand profile

CYC

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

Bound to: VK055_5071 — diguanylate cyclase domain protein

Via homolog PDB 4bwi UniProt Q55434 Formula C₃₃H₄₀N₄O₆
Mol. weight 588.71 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CYC
PDB
4bwi
UniProt (similar protein)
Q55434
Target protein
VK055_5071

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 588.71 Da
LogP (Crippen) 5.19
H-bond donors 5
H-bond acceptors 5
TPSA 160.95 Ų
Rotatable bonds 11
Aromatic rings 1 / 4
Heavy atoms 43
Fraction sp³ C 0.42
Formula C₃₃H₄₀N₄O₆

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 160.9
  • −1 ≤ LogP ≤ 5 5.19
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 588.7
  • LogP ≤ 5 5.19
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 160.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@@H]\1[C@H](C(=O)N/C1=C\c2c(c(c([nH]2)/C=C\3/C(=C(C(=N3)/C=C\4/C(=C(C(=O)N4)CC)C)C)CCC(=O)O)CCC(=O)O)C)C
InChI 
InChI=1S/C33H40N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h13-15,19-20,35H,7-12H2,1-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-,28-15-/t19-,20-/m1/s1
InChIKey 
VXTXPYZGDQPMHK-GMXXPEQVSA-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
PF01590

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_5071.

PDB 4

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)