Ligand profile

C2F

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_31803 — glycine cleavage system aminomethyltransferase T

Via homolog PDB 3a8i UniProt P27248 Formula C₂₀H₂₅N₇O₆
Mol. weight 459.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C2F
PDB
3a8i
UniProt (similar protein)
P27248
Target protein
KP13_31803

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 459.46 Da
LogP (Crippen) -0.26
H-bond donors 7
H-bond acceptors 9
TPSA 202.77 Ų
Rotatable bonds 9
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 202.8
  • −1 ≤ LogP ≤ 5 -0.26
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 459.5
  • LogP ≤ 5 -0.26
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 202.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[N@@]1[C@H](CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
InChI 
InChI=1S/C20H25N7O6/c1-27-12(9-23-16-15(27)18(31)26-20(21)25-16)8-22-11-4-2-10(3-5-11)17(30)24-13(19(32)33)6-7-14(28)29/h2-5,12-13,22H,6-9H2,1H3,(H,24,30)(H,28,29)(H,32,33)(H4,21,23,25,26,31)/t12-,13-/m0/s1
InChIKey 
ZNOVTXRBGFNYRX-STQMWFEESA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01571' 'PF08669

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_31803.

PDB 4

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)