Ligand profile

ZINC4517559

Virtual-screening candidate from ZINC.

Bound to: KP13_00831 — Serine hydroxymethyltransferase

Via homolog UniProt P0A825 Formula C₁₉H₂₁N₇O₆
Tanimoto 0.59
Mol. weight 443.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4517559
UniProt (similar protein)
P0A825
Tanimoto
0.590
Target protein
KP13_00831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 443.42 Da
LogP (Crippen) 0.01
H-bond donors 7
H-bond acceptors 9
TPSA 211.89 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.26
Formula C₁₉H₂₁N₇O₆

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 211.9
  • −1 ≤ LogP ≤ 5 0.01
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 443.4
  • LogP ≤ 5 0.01
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 211.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(c(=O)[nH]1)N=C(CNc1ccc(C(=O)N[C@H](CCC(=O)O)C(=O)O)cc1)CN2
InChI 
InChI=1S/C19H21N7O6/c20-19-25-15-14(17(30)26-19)23-11(8-22-15)7-21-10-3-1-9(2-4-10)16(29)24-12(18(31)32)5-6-13(27)28/h1-4,12,21H,5-8H2,(H,24,29)(H,27,28)(H,31,32)(H4,20,22,25,26,30)/t12-/m1/s1
InChIKey 
OZRNSSUDZOLUSN-GFCCVEGCSA-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)