Ligand profile

ZINC8618631

Virtual-screening candidate from ZINC.

Bound to: KP13_00831 — Serine hydroxymethyltransferase

Via homolog UniProt P0A825 Formula C₂₀H₂₅N₇O₆
Tanimoto 0.63
Mol. weight 459.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC8618631
UniProt (similar protein)
P0A825
Tanimoto
0.628
Target protein
KP13_00831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 459.46 Da
LogP (Crippen) 0.11
H-bond donors 8
H-bond acceptors 9
TPSA 211.56 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 33
Fraction sp³ C 0.35
Formula C₂₀H₂₅N₇O₆

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 211.6
  • −1 ≤ LogP ≤ 5 0.11
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 459.5
  • LogP ≤ 5 0.11
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 211.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(c(=O)[nH]1)N[C@H](CCNc1ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc1)CN2
InChI 
InChI=1S/C20H25N7O6/c21-20-26-16-15(18(31)27-20)24-12(9-23-16)7-8-22-11-3-1-10(2-4-11)17(30)25-13(19(32)33)5-6-14(28)29/h1-4,12-13,22,24H,5-9H2,(H,25,30)(H,28,29)(H,32,33)(H4,21,23,26,27,31)/t12-,13+/m1/s1
InChIKey 
SVEJTXIHPDUQLZ-OLZOCXBDSA-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)