Ligand profile

A2R

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

Bound to: VK055_1249 — gdhA

Via homolog PDB 7ecr UniProt T2D1F5 Formula C₁₅H₂₄N₅O₁₇P₃
Mol. weight 639.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A2R
PDB
7ecr
UniProt (similar protein)
T2D1F5
Target protein
VK055_1249

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 639.30 Da
LogP (Crippen) -3.17
H-bond donors 9
H-bond acceptors 18
TPSA 338.05 Ų
Rotatable bonds 11
Aromatic rings 2 / 4
Heavy atoms 40
Fraction sp³ C 0.67
Formula C₁₅H₂₄N₅O₁₇P₃

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 338.0
  • −1 ≤ LogP ≤ 5 -3.17
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 639.3
  • LogP ≤ 5 -3.17
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 338.0
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]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)OP(=O)(O)O)N
InChI 
InChI=1S/C15H24N5O17P3/c16-12-7-13(18-3-17-12)20(4-19-7)14-11(36-38(25,26)27)9(22)6(34-14)2-33-40(30,31)37-39(28,29)32-1-5-8(21)10(23)15(24)35-5/h3-6,8-11,14-15,21-24H,1-2H2,(H,28,29)(H,30,31)(H2,16,17,18)(H2,25,26,27)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
InChIKey 
ICNHOLCERMYLRZ-KEOHHSTQSA-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
PF00208' 'PF02812

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_1249.

PDB 6

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)