Ligand profile

LLD

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

Bound to: VK055_3742 — peptidyl-prolyl cis-trans isomerase in protein folding

Via homolog PDB 6o4a UniProt Q3JK38 Formula C₂₁H₂₅N₃O₅S
Mol. weight 431.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LLD
PDB
6o4a
UniProt (similar protein)
Q3JK38
Target protein
VK055_3742

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 431.51 Da
LogP (Crippen) 1.74
H-bond donors 1
H-bond acceptors 6
TPSA 105.67 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 30
Fraction sp³ C 0.38
Formula C₂₁H₂₅N₃O₅S

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 105.7
  • −1 ≤ LogP ≤ 5 1.74
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 431.5
  • LogP ≤ 5 1.74
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 105.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)CS(=O)(=O)N2CCCC[C@H]2C(=O)OCCNC(=O)c3cccnc3
InChI 
InChI=1S/C21H25N3O5S/c25-20(18-9-6-11-22-15-18)23-12-14-29-21(26)19-10-4-5-13-24(19)30(27,28)16-17-7-2-1-3-8-17/h1-3,6-9,11,15,19H,4-5,10,12-14,16H2,(H,23,25)/t19-/m0/s1
InChIKey 
YBYJEZJXJIOQAP-IBGZPJMESA-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
PF00254

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_3742.

PDB 9

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

Ligand PDB entry

ChEMBL 2

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)