Ligand profile

6MB

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

Bound to: VK055_3890 — dihydropteroate synthase

Via homolog PDB 5jq9 UniProt A0A2S9PLG4 Formula C₁₈H₁₈N₈O₄S
Mol. weight 442.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6MB
PDB
5jq9
UniProt (similar protein)
A0A2S9PLG4
Target protein
VK055_3890

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 442.46 Da
LogP (Crippen) 1.31
H-bond donors 4
H-bond acceptors 10
TPSA 181.78 Ų
Rotatable bonds 6
Aromatic rings 4 / 4
Heavy atoms 31
Fraction sp³ C 0.17
Formula C₁₈H₁₈N₈O₄S

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 181.8
  • −1 ≤ LogP ≤ 5 1.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 442.5
  • LogP ≤ 5 1.31
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 181.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(noc1NS(=O)(=O)c2ccc(cc2)NCc3cnc4c(n3)C(=O)NC(=N4)N)C
InChI 
InChI=1S/C18H18N8O4S/c1-9-10(2)25-30-17(9)26-31(28,29)13-5-3-11(4-6-13)20-7-12-8-21-15-14(22-12)16(27)24-18(19)23-15/h3-6,8,20,26H,7H2,1-2H3,(H3,19,21,23,24,27)
InChIKey 
JJZFSJXETRBCPR-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
PF00809

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_3890.

PDB 48

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

Ligand PDB entry

ChEMBL 25

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)