Ligand profile

SIB

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

Bound to: VK055_0432 — amidohydrolase family protein

Via homolog PDB 2plm UniProt Q9X034 Formula C₁₄H₁₉N₅O₆S
Mol. weight 385.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SIB
PDB
2plm
UniProt (similar protein)
Q9X034
Target protein
VK055_0432

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 385.40 Da
LogP (Crippen) -1.73
H-bond donors 5
H-bond acceptors 10
TPSA 176.58 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.57
Formula C₁₄H₁₉N₅O₆S

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 176.6
  • −1 ≤ LogP ≤ 5 -1.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 385.4
  • LogP ≤ 5 -1.73
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 176.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N=CNC2=O
InChI 
InChI=1S/C14H19N5O6S/c15-6(14(23)24)1-2-26-3-7-9(20)10(21)13(25-7)19-5-18-8-11(19)16-4-17-12(8)22/h4-7,9-10,13,20-21H,1-3,15H2,(H,23,24)(H,16,17,22)/t6-,7+,9+,10+,13+/m0/s1
InChIKey 
VNPWVMVYUSNFAW-WFMPWKQPSA-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_0432.

PDB 6

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)