Ligand profile

PP9

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

Bound to: VK055_1428 — heme-containing peroxidase/deferrochelatase

Via homolog PDB 2y4e UniProt P31545 Formula C₃₄H₃₄N₄O₄
Mol. weight 562.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PP9
PDB
2y4e
UniProt (similar protein)
P31545
Target protein
VK055_1428

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 562.67 Da
LogP (Crippen) 7.50
H-bond donors 4
H-bond acceptors 4
TPSA 131.96 Ų
Rotatable bonds 8
Aromatic rings 3 / 5
Heavy atoms 42
Fraction sp³ C 0.24
Formula C₃₄H₃₄N₄O₄

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 132.0
  • −1 ≤ LogP ≤ 5 7.50
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 562.7
  • LogP ≤ 5 7.50
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 132.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c2\cc\3/nc(\cc/4\c(c(/c(/[nH]4)c/c5n/c(c\c(c1CCC(=O)O)[nH]2)/C(=C5C)CCC(=O)O)C=C)C)C(=C3C)C=C
InChI 
InChI=1S/C34H34N4O4/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25/h7-8,13-16,36-37H,1-2,9-12H2,3-6H3,(H,39,40)(H,41,42)
InChIKey 
FEDYMSUPMFCVOD-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
PF20628

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_1428.

PDB 2

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

Ligand PDB entry