Binder profile

AP5

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

Bound to: PA3686 — adenylate kinase

Via homolog PDB 3x2s UniProt A0A0J9X1X4 C20H29N10O22P5
Mol. weight 916.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AP5
PDB
3x2s
UniProt (similar protein)
A0A0J9X1X4
Target protein
PA3686

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 916.37 Da
LogP (Crippen) -2.33
H-bond donors 11
H-bond acceptors 27
TPSA 480.50 Ų
Rotatable bonds 16
Aromatic rings 4 / 6
Heavy atoms 57
Fraction sp³ C 0.50
Formula C20H29N10O22P5

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.

Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 916.4
  • LogP ≤ 5 -2.33
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 27
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 480.5
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]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N
InChI 
InChI=1S/C20H29N10O22P5/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(47-19)1-45-53(35,36)49-55(39,40)51-57(43,44)52-56(41,42)50-54(37,38)46-2-8-12(32)14(34)20(48-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H,43,44)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKey 
OIMACDRJUANHTJ-XPWFQUROSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00406' 'PF05191

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3686.

PDB 4

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)