Ligand profile

2BO

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

Bound to: KP13_00831 — Serine hydroxymethyltransferase

Via homolog PDB 4wxg UniProt Q5M0B4 Formula C₁₂H₁₉N₂O₈P
Mol. weight 350.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2BO
PDB
4wxg
UniProt (similar protein)
Q5M0B4
Target protein
KP13_00831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 350.26 Da
LogP (Crippen) -0.37
H-bond donors 6
H-bond acceptors 7
TPSA 169.44 Ų
Rotatable bonds 8
Aromatic rings 1 / 1
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₂H₁₉N₂O₈P

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 -0.37
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 350.3
  • LogP ≤ 5 -0.37
  • 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]([C@@H](C)O)C(=O)O)O
InChI 
InChI=1S/C12H19N2O8P/c1-6-11(16)9(4-14-10(7(2)15)12(17)18)8(3-13-6)5-22-23(19,20)21/h3,7,10,14-16H,4-5H2,1-2H3,(H,17,18)(H2,19,20,21)/t7-,10+/m1/s1
InChIKey 
IZWQBQLGLAKRMN-XCBNKYQSSA-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)