Ligand profile

3NZ

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

Bound to: VK055_0207 — peptidyl-tRNA hydrolase

Via homolog PDB 4qbk UniProt Q9HVC3 Formula C₂₀H₂₅N₇O₅
Mol. weight 443.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3NZ
PDB
4qbk
UniProt (similar protein)
Q9HVC3
Target protein
VK055_0207

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 443.46 Da
LogP (Crippen) -1.28
H-bond donors 5
H-bond acceptors 11
TPSA 183.66 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 32
Fraction sp³ C 0.40
Formula C₂₀H₂₅N₇O₅

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 183.7
  • −1 ≤ LogP ≤ 5 -1.28
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 443.5
  • LogP ≤ 5 -1.28
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 183.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(cc1)C[C@@H](C(=O)N[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)CO)N
InChI 
InChI=1S/C20H25N7O5/c1-31-11-4-2-10(3-5-11)6-12(21)19(30)26-14-13(7-28)32-20(16(14)29)27-9-25-15-17(22)23-8-24-18(15)27/h2-5,8-9,12-14,16,20,28-29H,6-7,21H2,1H3,(H,26,30)(H2,22,23,24)/t12-,13+,14+,16+,20+/m0/s1
InChIKey 
FEUXXQHFLIJGOX-GJIZYBQMSA-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
PF01195

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_0207.

PDB 9

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)