Ligand profile

3H9

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

Bound to: VK055_3135 — fatty oxidation complex, alpha subunit FadB

Via homolog PDB 3zwa UniProt P07896 Formula C₂₇H₄₂N₇O₁₈P₃S⁴⁻
Mol. weight 877.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3H9
PDB
3zwa
UniProt (similar protein)
P07896
Target protein
VK055_3135

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 877.65 Da
LogP (Crippen) -3.31
H-bond donors 6
H-bond acceptors 24
TPSA 395.18 Ų
Rotatable bonds 23
Aromatic rings 2 / 3
Heavy atoms 56
Fraction sp³ C 0.70
Formula C₂₇H₄₂N₇O₁₈P₃S⁴⁻

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 395.2
  • −1 ≤ LogP ≤ 5 -3.31
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 877.7
  • LogP ≤ 5 -3.31
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 24
Veber's rules Fail
  • Rotatable bonds ≤ 10 23
  • TPSA ≤ 140 Ų 395.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)([O-])[O-])O)O
InChI 
InChI=1S/C27H46N7O18P3S/c1-4-5-15(35)10-18(37)56-9-8-29-17(36)6-7-30-25(40)22(39)27(2,3)12-49-55(46,47)52-54(44,45)48-11-16-21(51-53(41,42)43)20(38)26(50-16)34-14-33-19-23(28)31-13-32-24(19)34/h13-16,20-22,26,35,38-39H,4-12H2,1-3H3,(H,29,36)(H,30,40)(H,44,45)(H,46,47)(H2,28,31,32)(H2,41,42,43)/p-4/t15-,16+,20+,21+,22-,26+/m0/s1
InChIKey 
VAAHKRMGOFIORX-IKTBLOROSA-J

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
PF00378' 'PF02737

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_3135.

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)