Ligand profile

PLS

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

Bound to: KP13_00831 — Serine hydroxymethyltransferase

Via homolog PDB 6ymf UniProt I7H6W6 Formula C₁₁H₁₇N₂O₈P
Mol. weight 336.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PLS
PDB
6ymf
UniProt (similar protein)
I7H6W6
Target protein
KP13_00831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 336.24 Da
LogP (Crippen) -0.76
H-bond donors 6
H-bond acceptors 7
TPSA 169.44 Ų
Rotatable bonds 8
Aromatic rings 1 / 1
Heavy atoms 22
Fraction sp³ C 0.45
Formula C₁₁H₁₇N₂O₈P

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 -0.76
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 336.2
  • LogP ≤ 5 -0.76
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • 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](CO)C(=O)O)O
InChI 
InChI=1S/C11H17N2O8P/c1-6-10(15)8(3-13-9(4-14)11(16)17)7(2-12-6)5-21-22(18,19)20/h2,9,13-15H,3-5H2,1H3,(H,16,17)(H2,18,19,20)/t9-/m0/s1
InChIKey 
ODVKKQWXKRZJLG-VIFPVBQESA-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
PF00464

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_00831.

PDB 11

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)