Ligand profile

HDD

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

Bound to: VK055_0778 — bacterial Cytochrome Ubiquinol Oxidase family protein

Via homolog PDB 5doq UniProt A4IKP6 Formula C₃₄H₃₂FeN₄O₅
Mol. weight 632.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HDD
PDB
5doq
UniProt (similar protein)
A4IKP6
Target protein
VK055_0778

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 632.50 Da
LogP (Crippen) 3.21
H-bond donors 2
H-bond acceptors 8
TPSA 101.86 Ų
Rotatable bonds 5
Aromatic rings 3 / 9
Heavy atoms 44
Fraction sp³ C 0.29
Formula C₃₄H₃₂FeN₄O₅

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 101.9
  • −1 ≤ LogP ≤ 5 3.21
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 632.5
  • LogP ≤ 5 3.21
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 101.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c2n3c(c1CCC(=O)O)C=C4[C@]5(CCC(=O)O5)[C@@](C6=Cc7c(c(c8n7[Fe]3(N64)N9C(=C2)C(=C(C9=C8)C=C)C)C)C=C)(C)O
InChI 
InChI=1S/C34H32N4O5.Fe/c1-7-20-17(3)23-13-24-19(5)22(9-10-31(39)40)28(37-24)16-30-34(12-11-32(41)43-34)33(6,42)29(38-30)15-27-21(8-2)18(4)25(36-27)14-26(20)35-23;/h7-8,13-16,42H,1-2,9-12H2,3-6H3,(H,39,40);/q-4;+4/t33-,34+;/m0./s1
InChIKey 
UMGOPAWIGKFTRK-XCVPDAMTSA-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
PF01654

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_0778.

PDB 4

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)