Ligand profile

IN5

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

Bound to: VK055_4046 — cystathionine beta-lyase

Via homolog PDB 4itx UniProt P06721 Formula C₁₀H₁₈N₂O₈P₂
Mol. weight 356.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
IN5
PDB
4itx
UniProt (similar protein)
P06721
Target protein
VK055_4046

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 356.21 Da
LogP (Crippen) 0.32
H-bond donors 6
H-bond acceptors 6
TPSA 169.44 Ų
Rotatable bonds 7
Aromatic rings 1 / 1
Heavy atoms 22
Fraction sp³ C 0.50
Formula C₁₀H₁₈N₂O₈P₂

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 169.4
  • −1 ≤ LogP ≤ 5 0.32
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 356.2
  • LogP ≤ 5 0.32
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 169.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](C)P(=O)(O)O)O
InChI 
InChI=1S/C10H18N2O8P2/c1-6-10(13)9(4-12-7(2)21(14,15)16)8(3-11-6)5-20-22(17,18)19/h3,7,12-13H,4-5H2,1-2H3,(H2,14,15,16)(H2,17,18,19)/t7-/m1/s1
InChIKey 
WHDCJKAOZPBUAY-SSDOTTSWSA-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
PF01053

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_4046.

PDB 16

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

Ligand PDB entry

ChEMBL 4

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)