Ligand profile

ZINC1560405340

Virtual-screening candidate from ZINC.

Bound to: KP13_31803 — glycine cleavage system aminomethyltransferase T

Via homolog UniProt Q9WY54 Formula C₂₀H₂₂N₇O₇
Tanimoto 0.56
Mol. weight 472.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1560405340
UniProt (similar protein)
Q9WY54
Tanimoto
0.561
Target protein
KP13_31803

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 472.44 Da
LogP (Crippen) -0.16
H-bond donors 7
H-bond acceptors 10
TPSA 220.10 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 34
Fraction sp³ C 0.25
Formula C₂₀H₂₂N₇O₇

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 -0.16
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 472.4
  • LogP ≤ 5 -0.16
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • 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](CCC(=O)O)C(=O)O)cc1)N2C=O
InChI 
InChI=1S/C20H22N7O7/c21-20-25-16-15(18(32)26-20)27(9-28)12(8-23-16)7-22-11-3-1-10(2-4-11)17(31)24-13(19(33)34)5-6-14(29)30/h1-4,9,12,22H,5-8H2,(H,24,31)(H,29,30)(H,33,34)(H4,21,23,25,26,32)/t12-/m0/s1
InChIKey 
IBEDLJVBVQHGAR-LBPRGKRZSA-N

Provenance

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

Method
LigQ nearest_k
Query
FFO
Homolog
Q9WY54

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 5

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)