Ligand profile

AV2

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

Bound to: KP13_02403 — Adenylyl-sulfate kinase

Via homolog PDB 1m7g UniProt Q12657 Formula C₁₀H₁₄N₅O₁₂P₂V
Mol. weight 509.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AV2
PDB
1m7g
UniProt (similar protein)
Q12657
Target protein
KP13_02403

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 509.14 Da
LogP (Crippen) -1.45
H-bond donors 5
H-bond acceptors 13
TPSA 247.90 Ų
Rotatable bonds 6
Aromatic rings 2 / 4
Heavy atoms 30
Fraction sp³ C 0.50
Formula C₁₀H₁₄N₅O₁₂P₂V

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 247.9
  • −1 ≤ LogP ≤ 5 -1.45
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 509.1
  • LogP ≤ 5 -1.45
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 247.9
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)CO[P@](=O)(O)OP(=O)(O)O)O[V](=O)(O4)O)N
InChI 
InChI=1S/C10H13N5O10P2.H2O.O.V/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20;;;/h2-4,6-7,10H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20);1H2;;/q-2;;;+3/p-1/t4-,6-,7-,10-;;;/m1.../s1
InChIKey 
PCCLXHWRDHBBRF-MSQVLRTGSA-M

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
PF01583

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02403.

PDB 7

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)