Ligand profile

3Y8

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

Bound to: VK055_4335 — precorrin-6x reductase

Via homolog PDB 4x7g UniProt O68098 Formula C₄₅H₆₀N₄O₁₆
Mol. weight 912.99 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3Y8
PDB
4x7g
UniProt (similar protein)
O68098
Target protein
VK055_4335

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 912.99 Da
LogP (Crippen) 4.09
H-bond donors 10
H-bond acceptors 12
TPSA 347.18 Ų
Rotatable bonds 19
Aromatic rings 0 / 5
Heavy atoms 65
Fraction sp³ C 0.64
Formula C₄₅H₆₀N₄O₁₆

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 4.09
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 913.0
  • LogP ≤ 5 4.09
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 19
  • TPSA ≤ 140 Ų 347.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=C2[C@H]([C@]([C@@](N2)([C@H]3[C@@H]([C@@]([C@@H](N3)CC4=N[C@@](CC5=NC1[C@@](C5CCC(=O)O)(C)CC(=O)O)(C(=C4CCC(=O)O)CC(=O)O)C)(C)C=CC(=O)O)CC(=O)O)C)(C)CC(=O)O)CCC(=O)O
InChI 
InChI=1S/C45H60N4O16/c1-21-38-24(9-12-32(54)55)43(4,20-37(64)65)45(6,49-38)40-26(16-35(60)61)41(2,14-13-33(56)57)29(47-40)17-27-22(7-10-30(50)51)25(15-34(58)59)44(5,48-27)18-28-23(8-11-31(52)53)42(3,19-36(62)63)39(21)46-28/h13-14,23-24,26,29,39-40,47,49H,7-12,15-20H2,1-6H3,(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)(H,64,65)/t23?,24-,26+,29+,39?,40-,41-,42+,43+,44+,45+/m1/s1
InChIKey 
DZSBRGWVIYKASI-HWNQECFSSA-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
PF02571

External resources

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