Ligand profile

ZINC13887836

Virtual-screening candidate from ZINC.

Bound to: KP13_00831 — Serine hydroxymethyltransferase

Via homolog UniProt P0A825 Formula C₂₀H₂₃N₅O₆
Tanimoto 0.58
Mol. weight 429.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13887836
UniProt (similar protein)
P0A825
Tanimoto
0.577
Target protein
KP13_00831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 429.43 Da
LogP (Crippen) 0.54
H-bond donors 6
H-bond acceptors 7
TPSA 187.50 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.35
Formula C₂₀H₂₃N₅O₆

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 187.5
  • −1 ≤ LogP ≤ 5 0.54
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 429.4
  • LogP ≤ 5 0.54
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 187.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(c(=O)[nH]1)[C@@H](CCc1ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc1)CN2
InChI 
InChI=1S/C20H23N5O6/c21-20-24-16-15(18(29)25-20)12(9-22-16)6-3-10-1-4-11(5-2-10)17(28)23-13(19(30)31)7-8-14(26)27/h1-2,4-5,12-13H,3,6-9H2,(H,23,28)(H,26,27)(H,30,31)(H4,21,22,24,25,29)/t12-,13-/m0/s1
InChIKey 
WIQHGSZNXPONNQ-STQMWFEESA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Query
FFO
Homolog
P0A825

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 12

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)