Ligand profile

3LM

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

Bound to: KP13_02775 — Cystathionine beta-lyase metC

Via homolog PDB 3aeo UniProt Q86D28 Formula C₁₃H₁₉N₂O₇PS
Mol. weight 378.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3LM
PDB
3aeo
UniProt (similar protein)
Q86D28
Target protein
KP13_02775

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 378.34 Da
LogP (Crippen) 1.13
H-bond donors 5
H-bond acceptors 7
TPSA 149.21 Ų
Rotatable bonds 9
Aromatic rings 1 / 1
Heavy atoms 24
Fraction sp³ C 0.38
Formula C₁₃H₁₉N₂O₇PS

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 149.2
  • −1 ≤ LogP ≤ 5 1.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 378.3
  • LogP ≤ 5 1.13
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 149.2
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(=C/CSC)/C(=O)O)O
InChI 
InChI=1S/C13H19N2O7PS/c1-8-12(16)10(6-15-11(13(17)18)3-4-24-2)9(5-14-8)7-22-23(19,20)21/h3,5,15-16H,4,6-7H2,1-2H3,(H,17,18)(H2,19,20,21)/b11-3+
InChIKey 
LPFNPHQQDYAHKU-QDEBKDIKSA-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 KP13_02775.

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)