Ligand profile

DJM

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

Bound to: VK055_4003 — urease, alpha subunit

Via homolog PDB 6zja UniProt P69996 Formula C₁₃H₁₅N₃O₂S
Mol. weight 277.35 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DJM
PDB
6zja
UniProt (similar protein)
P69996
Target protein
VK055_4003

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 277.35 Da
LogP (Crippen) 2.09
H-bond donors 2
H-bond acceptors 5
TPSA 67.15 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 19
Fraction sp³ C 0.23
Formula C₁₃H₁₅N₃O₂S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 67.2
  • −1 ≤ LogP ≤ 5 2.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 277.3
  • LogP ≤ 5 2.09
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 67.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(cc(c1)n2ccnc2SCC(=O)NO)C
InChI 
InChI=1S/C13H15N3O2S/c1-9-5-10(2)7-11(6-9)16-4-3-14-13(16)19-8-12(17)15-18/h3-7,18H,8H2,1-2H3,(H,15,17)
InChIKey 
KKPWLEDZKPGXQJ-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
PF01979

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_4003.

PDB 8

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)