Ligand profile

BLP

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

Bound to: VK055_4046 — cystathionine beta-lyase

Via homolog PDB 2gqn UniProt P06721 Formula C₁₇H₂₀N₅O₉P
Mol. weight 469.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BLP
PDB
2gqn
UniProt (similar protein)
P06721
Target protein
VK055_4046

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 469.35 Da
LogP (Crippen) 0.16
H-bond donors 6
H-bond acceptors 9
TPSA 213.25 Ų
Rotatable bonds 10
Aromatic rings 2 / 2
Heavy atoms 32
Fraction sp³ C 0.24
Formula C₁₇H₂₀N₅O₉P

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 213.2
  • −1 ≤ LogP ≤ 5 0.16
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 469.3
  • LogP ≤ 5 0.16
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 213.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CNNC(=O)CNC(=O)c2ccccc2[N+](=O)[O-])O
InChI 
InChI=1S/C17H20N5O9P/c1-10-16(24)13(11(6-18-10)9-31-32(28,29)30)7-20-21-15(23)8-19-17(25)12-4-2-3-5-14(12)22(26)27/h2-6,20,24H,7-9H2,1H3,(H,19,25)(H,21,23)(H2,28,29,30)
InChIKey 
AJHNLRARXNOGMZ-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
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)