Ligand profile

UP2

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

Bound to: VK055_4401 — cysG

Via homolog PDB 2ybq UniProt P95417 Formula C₄₀H₄₄N₄O₁₆
Mol. weight 836.80 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
UP2
PDB
2ybq
UniProt (similar protein)
P95417
Target protein
VK055_4401

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 836.80 Da
LogP (Crippen) 2.25
H-bond donors 12
H-bond acceptors 8
TPSA 361.56 Ų
Rotatable bonds 20
Aromatic rings 4 / 5
Heavy atoms 60
Fraction sp³ C 0.40
Formula C₄₀H₄₄N₄O₁₆

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 361.6
  • −1 ≤ LogP ≤ 5 2.25
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 836.8
  • LogP ≤ 5 2.25
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 361.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1c2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc4c(c(c([nH]4)Cc5c(c(c1[nH]5)CCC(=O)O)CC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O
InChI 
InChI=1S/C40H44N4O16/c45-33(46)5-1-17-21(9-37(53)54)29-14-27-19(3-7-35(49)50)22(10-38(55)56)30(43-27)15-28-20(4-8-36(51)52)24(12-40(59)60)32(44-28)16-31-23(11-39(57)58)18(2-6-34(47)48)26(42-31)13-25(17)41-29/h41-44H,1-16H2,(H,45,46)(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)
InChIKey 
HUHWZXWWOFSFKF-UHFFFAOYSA-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
PF00590

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_4401.

PDB 3

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

Ligand PDB entry