Ligand profile

39S

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

Bound to: VK055_3151 — 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase

Via homolog PDB 4qqu UniProt P82610 Formula C₂₉H₃₇N₉O₁₂
Mol. weight 703.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
39S
PDB
4qqu
UniProt (similar protein)
P82610
Target protein
VK055_3151

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 703.67 Da
LogP (Crippen) -1.58
H-bond donors 12
H-bond acceptors 13
TPSA 344.36 Ų
Rotatable bonds 19
Aromatic rings 2 / 3
Heavy atoms 50
Fraction sp³ C 0.41
Formula C₂₉H₃₇N₉O₁₂

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 344.4
  • −1 ≤ LogP ≤ 5 -1.58
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 703.7
  • LogP ≤ 5 -1.58
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 19
  • TPSA ≤ 140 Ų 344.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)NC[C@H]2CNC3=C(N2)C(=O)NC(=N3)N
InChI 
InChI=1S/C29H37N9O12/c30-29-37-23-22(25(44)38-29)33-15(12-32-23)11-31-14-3-1-13(2-4-14)24(43)36-18(28(49)50)6-9-20(40)34-16(26(45)46)5-8-19(39)35-17(27(47)48)7-10-21(41)42/h1-4,15-18,31,33H,5-12H2,(H,34,40)(H,35,39)(H,36,43)(H,41,42)(H,45,46)(H,47,48)(H,49,50)(H4,30,32,37,38,44)/t15-,16-,17-,18-/m0/s1
InChIKey 
RXWVHRYZTWZATH-XSLAGTTESA-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
PF01717' 'PF08267

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3151.

PDB 5

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)