Ligand profile

MDE

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

Bound to: KP13_03218 — Glutamate synthase [NADPH] small chain

Via homolog PDB 1ps9 UniProt P42593 Formula C₃₃H₅₅N₇O₁₈P₃S₂⁺
Mol. weight 994.89 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MDE
PDB
1ps9
UniProt (similar protein)
P42593
Target protein
KP13_03218

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 994.89 Da
LogP (Crippen) 0.91
H-bond donors 10
H-bond acceptors 20
TPSA 382.55 Ų
Rotatable bonds 30
Aromatic rings 2 / 3
Heavy atoms 63
Fraction sp³ C 0.67
Formula C₃₃H₅₅N₇O₁₈P₃S₂⁺

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 382.6
  • −1 ≤ LogP ≤ 5 0.91
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 994.9
  • LogP ≤ 5 0.91
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 30
  • TPSA ≤ 140 Ų 382.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCC[C@@H](C\C=C\C(=O)SCCNC(=O)CCNC(C(=O)C(C)(C)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)[n+]2c[nH]c3c2ncnc3N)O)OP(=O)(O)O)O)SCC=O
InChI 
InChI=1S/C33H54N7O18P3S2/c1-4-5-6-8-21(62-16-14-41)9-7-10-24(43)63-15-13-35-23(42)11-12-36-31(46)28(45)33(2,3)18-55-61(52,53)58-60(50,51)54-17-22-27(57-59(47,48)49)26(44)32(56-22)40-20-39-25-29(34)37-19-38-30(25)40/h7,10,14,19-22,26-27,31-32,36,44,46H,4-6,8-9,11-13,15-18H2,1-3H3,(H7,34,35,37,38,42,47,48,49,50,51,52,53)/p+1/b10-7+/t21-,22+,26+,27+,31?,32+/m0/s1
InChIKey 
IJSMUHMCIYOVMM-KPWYCAMOSA-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
PF00724' 'PF07992

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_03218.

PDB 4

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

Ligand PDB entry

ZINC 28

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

Compound Similarity (Tanimoto)