Binder profile

AFH

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

Bound to: PA5012 — heptosyltransferase II

Via homolog PDB 2h1h UniProt P24173 C17H26FN5O15P2
Mol. weight 621.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AFH
PDB
2h1h
UniProt (similar protein)
P24173
Target protein
PA5012

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 621.36 Da
LogP (Crippen) -3.58
H-bond donors 9
H-bond acceptors 18
TPSA 311.75 Ų
Rotatable bonds 10
Aromatic rings 2 / 4
Heavy atoms 40
Fraction sp³ C 0.71
Formula C17H26FN5O15P2

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 621.4
  • LogP ≤ 5 -3.58
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 311.7
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)O[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)[C@H](CO)O)O)O)F)O)O)N
InChI 
InChI=1S/C17H26FN5O15P2/c18-7-10(27)11(28)13(5(25)1-24)36-17(7)37-40(32,33)38-39(30,31)34-2-6-9(26)12(29)16(35-6)23-4-22-8-14(19)20-3-21-15(8)23/h3-7,9-13,16-17,24-29H,1-2H2,(H,30,31)(H,32,33)(H2,19,20,21)/t5-,6+,7+,9+,10+,11-,12+,13+,16+,17-/m0/s1
InChIKey 
SUPCMUQXGKOKIM-FJBXLJLUSA-N

Provenance

Annotation context from LigQ_2 search.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01075

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA5012.

ZINC 50

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

Compound Similarity (Tanimoto)