Ligand profile

PMT

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

Bound to: VK055_3490 — phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase

Via homolog PDB 1u7z UniProt P0ABQ0 Formula C₁₈H₃₀N₄O₁₅P₂
Mol. weight 604.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PMT
PDB
1u7z
UniProt (similar protein)
P0ABQ0
Target protein
VK055_3490

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 604.40 Da
LogP (Crippen) -2.89
H-bond donors 8
H-bond acceptors 15
TPSA 299.52 Ų
Rotatable bonds 13
Aromatic rings 1 / 2
Heavy atoms 39
Fraction sp³ C 0.67
Formula C₁₈H₃₀N₄O₁₅P₂

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 299.5
  • −1 ≤ LogP ≤ 5 -2.89
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 604.4
  • LogP ≤ 5 -2.89
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 299.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)O
InChI 
InChI=1S/C18H30N4O15P2/c1-18(2,8-35-38(29,30)31)14(26)15(27)20-5-3-11(23)37-39(32,33)34-7-9-12(24)13(25)16(36-9)22-6-4-10(19)21-17(22)28/h4,6,9,12-14,16,24-26H,3,5,7-8H2,1-2H3,(H,20,27)(H,32,33)(H2,19,21,28)(H2,29,30,31)/t9-,12-,13-,14+,16-/m1/s1
InChIKey 
JURRMAHLXBVXRF-FIEZRUJPSA-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
PF04127

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_3490.

PDB 2

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)