Ligand profile

FAQ

Ligand co-crystallized with this exact protein (Protein Data Bank).

Bound to: VK055_1041 — phenylacetic acid catabolic family protein

Direct evidence PDB 4iit UniProt A6T8I0 Formula C₂₉H₄₂N₇O₁₇P₃S
Mol. weight 885.68 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FAQ
PDB
4iit
UniProt (this protein)
A6T8I0
Target protein
VK055_1041

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 885.68 Da
LogP (Crippen) -0.09
H-bond donors 9
H-bond acceptors 19
TPSA 363.63 Ų
Rotatable bonds 21
Aromatic rings 3 / 4
Heavy atoms 57
Fraction sp³ C 0.52
Formula C₂₉H₄₂N₇O₁₇P₃S

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 363.6
  • −1 ≤ LogP ≤ 5 -0.09
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 885.7
  • LogP ≤ 5 -0.09
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 21
  • TPSA ≤ 140 Ų 363.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)Cc4ccccc4)O
InChI 
InChI=1S/C29H42N7O17P3S/c1-29(2,24(40)27(41)32-9-8-19(37)31-10-11-57-20(38)12-17-6-4-3-5-7-17)14-50-56(47,48)53-55(45,46)49-13-18-23(52-54(42,43)44)22(39)28(51-18)36-16-35-21-25(30)33-15-34-26(21)36/h3-7,15-16,18,22-24,28,39-40H,8-14H2,1-2H3,(H,31,37)(H,32,41)(H,45,46)(H,47,48)(H2,30,33,34)(H2,42,43,44)/t18-,22-,23-,24+,28-/m1/s1
InChIKey 
ZIGIFDRJFZYEEQ-CECATXLMSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF05138

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_1041.

PDB 2

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

Ligand PDB entry

ZINC 4

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)