Ligand profile

MGD

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

Bound to: KP13_03835 — Protein aegA

Via homolog PDB 1kqf UniProt P0AAJ3 Formula C₂₀H₂₆N₁₀O₁₃P₂S₂
Mol. weight 740.57 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MGD
PDB
1kqf
UniProt (similar protein)
P0AAJ3
Target protein
KP13_03835

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 740.57 Da
LogP (Crippen) -2.06
H-bond donors 12
H-bond acceptors 21
TPSA 346.63 Ų
Rotatable bonds 9
Aromatic rings 3 / 6
Heavy atoms 47
Fraction sp³ C 0.45
Formula C₂₀H₂₆N₁₀O₁₃P₂S₂

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 346.6
  • −1 ≤ LogP ≤ 5 -2.06
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 740.6
  • LogP ≤ 5 -2.06
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 21
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 346.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4C(=C([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C20H26N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-10,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1
InChIKey 
VQAGYJCYOLHZDH-ILXWUORBSA-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
PF00384' 'PF01568' 'PF04879

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_03835.

PDB 7

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)