Ligand profile

A7R

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

Bound to: KP13_00254 — Glyoxylate/hydroxypyruvate reductase B

Via homolog PDB 6ih3 UniProt G4XDR8 Formula C₂₀H₂₈N₅O₁₅P₂⁺
Mol. weight 640.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A7R
PDB
6ih3
UniProt (similar protein)
G4XDR8
Target protein
KP13_00254

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 640.41 Da
LogP (Crippen) -3.60
H-bond donors 8
H-bond acceptors 16
TPSA 309.55 Ų
Rotatable bonds 11
Aromatic rings 2 / 4
Heavy atoms 42
Fraction sp³ C 0.50
Formula C₂₀H₂₈N₅O₁₅P₂⁺

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 309.5
  • −1 ≤ LogP ≤ 5 -3.60
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 640.4
  • LogP ≤ 5 -3.60
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 309.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c[n+](c1)[C@@H]2[C@@H]([C@@H]([C@@H](O2)COP(=O)(O)OP(=O)(O)OC[C@H]3[C@H]([C@H]([C@H](O3)N4C=CC(=NC4=O)N)O)O)O)O)C(=O)N
InChI 
InChI=1S/C20H27N5O15P2/c21-12-3-5-25(20(31)23-12)19-16(29)14(27)11(39-19)8-37-42(34,35)40-41(32,33)36-7-10-13(26)15(28)18(38-10)24-4-1-2-9(6-24)17(22)30/h1-6,10-11,13-16,18-19,26-29H,7-8H2,(H5-,21,22,23,30,31,32,33,34,35)/p+1/t10-,11-,13+,14+,15+,16+,18-,19-/m0/s1
InChIKey 
CRWNYXSXULHVKY-JKHXZYGESA-O

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
PF00389' 'PF02826

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_00254.

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)