Ligand profile

ZINC8628601

Virtual-screening candidate from ZINC.

Bound to: KP13_00831 — Serine hydroxymethyltransferase

Via homolog UniProt P0A825 Formula C₂₁H₂₇N₇O₆
Tanimoto 0.59
Mol. weight 473.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC8628601
UniProt (similar protein)
P0A825
Tanimoto
0.593
Target protein
KP13_00831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 473.49 Da
LogP (Crippen) 0.13
H-bond donors 7
H-bond acceptors 9
TPSA 202.77 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 34
Fraction sp³ C 0.38
Formula C₂₁H₂₇N₇O₆

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 202.8
  • −1 ≤ LogP ≤ 5 0.13
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 473.5
  • LogP ≤ 5 0.13
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 202.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1c2c([nH]c(N)nc2=O)NC[C@H]1CCNc1ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc1
InChI 
InChI=1S/C21H27N7O6/c1-28-13(10-24-17-16(28)19(32)27-21(22)26-17)8-9-23-12-4-2-11(3-5-12)18(31)25-14(20(33)34)6-7-15(29)30/h2-5,13-14,23H,6-10H2,1H3,(H,25,31)(H,29,30)(H,33,34)(H4,22,24,26,27,32)/t13-,14+/m1/s1
InChIKey 
KCPBTDJBDDCNQE-KGLIPLIRSA-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)