Ligand profile

ZINC8997306

Virtual-screening candidate from ZINC.

Bound to: KP13_00831 — Serine hydroxymethyltransferase

Via homolog UniProt P0A825 Formula C₂₁H₂₅N₇O₇
Tanimoto 0.71
Mol. weight 487.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC8997306
UniProt (similar protein)
P0A825
Tanimoto
0.714
Target protein
KP13_00831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 487.47 Da
LogP (Crippen) 0.07
H-bond donors 7
H-bond acceptors 10
TPSA 220.10 Ų
Rotatable bonds 11
Aromatic rings 2 / 3
Heavy atoms 35
Fraction sp³ C 0.33
Formula C₂₁H₂₅N₇O₇

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 220.1
  • −1 ≤ LogP ≤ 5 0.07
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 487.5
  • LogP ≤ 5 0.07
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 220.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc(O)c2c(n1)NC[C@H](CNc1ccc(C(=O)N[C@H](CCCC(=O)O)C(=O)O)cc1)N2C=O
InChI 
InChI=1S/C21H25N7O7/c22-21-26-17-16(19(33)27-21)28(10-29)13(9-24-17)8-23-12-6-4-11(5-7-12)18(32)25-14(20(34)35)2-1-3-15(30)31/h4-7,10,13-14,23H,1-3,8-9H2,(H,25,32)(H,30,31)(H,34,35)(H4,22,24,26,27,33)/t13-,14+/m0/s1
InChIKey 
GOQSXAYRWFUXOD-UONOGXRCSA-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)