Ligand profile

TM1

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

Bound to: VK055_1741 — HAD ATPase, P-type, IC family protein

Via homolog PDB 3ar8 UniProt P04191-2 Formula C₁₆H₁₅N₈O₁₃P
Mol. weight 558.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TM1
PDB
3ar8
UniProt (similar protein)
P04191-2
Target protein
VK055_1741

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 558.31 Da
LogP (Crippen) -1.12
H-bond donors 3
H-bond acceptors 16
TPSA 293.49 Ų
Rotatable bonds 7
Aromatic rings 2 / 5
Heavy atoms 38
Fraction sp³ C 0.44
Formula C₁₆H₁₅N₈O₁₃P

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 293.5
  • −1 ≤ LogP ≤ 5 -1.12
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 558.3
  • LogP ≤ 5 -1.12
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 293.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@H]4[C@@H]([C@H](O3)COP(=O)(O)O)OC5(O4)C(=CC(C=C5[N+](=O)[O-])[N+](=O)[O-])[N+](=O)[O-])N
InChI 
InChI=1S/C16H15N8O13P/c17-13-10-14(19-4-18-13)21(5-20-10)15-12-11(7(35-15)3-34-38(31,32)33)36-16(37-12)8(23(27)28)1-6(22(25)26)2-9(16)24(29)30/h1-2,4-7,11-12,15H,3H2,(H2,17,18,19)(H2,31,32,33)/t6?,7-,11-,12-,15-,16?/m1/s1
InChIKey 
OHPXFACYTRBVRA-YKWNPASPSA-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
PF00122' 'PF00702' 'PF13246

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_1741.

PDB 27

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)