Ligand profile

4LM

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

Bound to: VK055_4046 — cystathionine beta-lyase

Via homolog PDB 3aep UniProt Q86D28 Formula C₁₂H₁₅N₂O₇P
Mol. weight 330.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4LM
PDB
3aep
UniProt (similar protein)
Q86D28
Target protein
VK055_4046

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 330.23 Da
LogP (Crippen) 1.11
H-bond donors 4
H-bond acceptors 6
TPSA 149.54 Ų
Rotatable bonds 6
Aromatic rings 1 / 1
Heavy atoms 22
Fraction sp³ C 0.25
Formula C₁₂H₁₅N₂O₇P

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 149.5
  • −1 ≤ LogP ≤ 5 1.11
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 330.2
  • LogP ≤ 5 1.11
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 149.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C/C=C(\C(=O)O)/N=C/c1c(cnc(c1O)C)COP(=O)(O)O
InChI 
InChI=1S/C12H15N2O7P/c1-3-10(12(16)17)14-5-9-8(6-21-22(18,19)20)4-13-7(2)11(9)15/h3-5,15H,6H2,1-2H3,(H,16,17)(H2,18,19,20)/b10-3+,14-5+
InChIKey 
BBYSOXSBJOWRNU-VMTXVVAMSA-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)