Ligand profile

C2E

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

Bound to: VK055_3105 — diguanylate cyclase domain protein

Via homolog PDB 6ttr UniProt A0A0H3CAN8 Formula C₂₀H₂₄N₁₀O₁₄P₂
Mol. weight 690.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C2E
PDB
6ttr
UniProt (similar protein)
A0A0H3CAN8
Target protein
VK055_3105

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 690.42 Da
LogP (Crippen) -3.05
H-bond donors 8
H-bond acceptors 20
TPSA 349.62 Ų
Rotatable bonds 2
Aromatic rings 4 / 7
Heavy atoms 46
Fraction sp³ C 0.50
Formula C₂₀H₂₄N₁₀O₁₄P₂

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 349.6
  • −1 ≤ LogP ≤ 5 -3.05
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 690.4
  • LogP ≤ 5 -3.05
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 349.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O)(O[C@@H]5[C@@H](CO[P@@](=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
InChIKey 
PKFDLKSEZWEFGL-MHARETSRSA-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
PF00990

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_3105.

PDB 3

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)