Ligand profile

DNB

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

Bound to: VK055_0569 — ribonucleoside hydrolase 1

Via homolog PDB 3mkn UniProt C3T3U2 Formula C₁₁H₁₇N₃O₃
Mol. weight 239.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DNB
PDB
3mkn
UniProt (similar protein)
C3T3U2
Target protein
VK055_0569

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 239.27 Da
LogP (Crippen) -1.42
H-bond donors 6
H-bond acceptors 6
TPSA 124.76 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.45
Formula C₁₁H₁₇N₃O₃

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 124.8
  • −1 ≤ LogP ≤ 5 -1.42
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 239.3
  • LogP ≤ 5 -1.42
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 124.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(cc1[C@H]2[C@@H]([C@@H]([C@H](N2)CO)O)O)N)N
InChI 
InChI=1S/C11H17N3O3/c12-6-2-1-5(3-7(6)13)9-11(17)10(16)8(4-15)14-9/h1-3,8-11,14-17H,4,12-13H2/t8-,9+,10-,11+/m1/s1
InChIKey 
YAYMFJWCRXEXGZ-YTWAJWBKSA-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
PF01156

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_0569.

PDB 5

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

Ligand PDB entry

ChEMBL 1

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)