Ligand profile

00A

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

Bound to: VK055_4857 — O-succinylbenzoate-CoA ligase

Via homolog PDB 3cw8 UniProt Q8GN86 Formula C₁₇H₁₇ClN₅O₈P
Mol. weight 485.78 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
00A
PDB
3cw8
UniProt (similar protein)
Q8GN86
Target protein
VK055_4857

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 485.78 Da
LogP (Crippen) 0.66
H-bond donors 4
H-bond acceptors 12
TPSA 192.14 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 32
Fraction sp³ C 0.29
Formula C₁₇H₁₇ClN₅O₈P

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 192.1
  • −1 ≤ LogP ≤ 5 0.66
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 485.8
  • LogP ≤ 5 0.66
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 192.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C(=O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)Cl
InChI 
InChI=1S/C17H17ClN5O8P/c18-9-3-1-8(2-4-9)17(26)31-32(27,28)29-5-10-12(24)13(25)16(30-10)23-7-22-11-14(19)20-6-21-15(11)23/h1-4,6-7,10,12-13,16,24-25H,5H2,(H,27,28)(H2,19,20,21)/t10-,12-,13-,16-/m1/s1
InChIKey 
RVDNKWBGRIIRML-XNIJJKJLSA-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
PF00501

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_4857.

PDB 11

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)