Ligand profile

SH0

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

Bound to: VK055_1488 — sulfur relay, TusE/DsrC/DsvC family protein

Via homolog PDB 2v4j UniProt P45573 Formula C₄₂H₅₂N₄O₁₆
Mol. weight 868.89 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SH0
PDB
2v4j
UniProt (similar protein)
P45573
Target protein
VK055_1488

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 868.89 Da
LogP (Crippen) 3.40
H-bond donors 10
H-bond acceptors 12
TPSA 347.18 Ų
Rotatable bonds 20
Aromatic rings 0 / 5
Heavy atoms 62
Fraction sp³ C 0.57
Formula C₄₂H₅₂N₄O₁₆

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 347.2
  • −1 ≤ LogP ≤ 5 3.40
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 868.9
  • LogP ≤ 5 3.40
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 347.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@]\1([C@@H](C2/C=C\3/[C@@]([C@@H](/C(=C/C4=N[C@H](C[C@H]5C(=C(C(=N5)/C=C1\N2)CC(=O)O)CCC(=O)O)[C@H]([C@@H]4CC(=O)O)CCC(=O)O)/N3)CCC(=O)O)(C)CC(=O)O)CCC(=O)O)CC(=O)O
InChI 
InChI=1S/C42H52N4O16/c1-41(17-39(59)60)23(5-9-35(51)52)29-14-27-21(11-37(55)56)19(3-7-33(47)48)25(43-27)13-26-20(4-8-34(49)50)22(12-38(57)58)28(44-26)15-31-42(2,18-40(61)62)24(6-10-36(53)54)30(46-31)16-32(41)45-29/h14-16,19,21,23-26,30,45-46H,3-13,17-18H2,1-2H3,(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H,61,62)/b29-14-,31-15-,32-16-/t19-,21-,23+,24+,25+,26-,30?,41-,42-/m0/s1
InChIKey 
PTDGOSZHGZMQAZ-UGDYZOJISA-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
PF01077' 'PF03460

External resources

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