Binder profile

C2E

Ligand co-crystallized with this exact protein (Protein Data Bank).

Bound to: PA3542 — alginate biosynthesis protein Alg44

Direct evidence PDB 4rt0 UniProt Q9HY69 C20H24N10O14P2
Mol. weight 690.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C2E
PDB
4rt0
UniProt (this protein)
Q9HY69
Target protein
PA3542

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 690.42 Da
LogP (Crippen) -3.05
H-bond donors 8
H-bond acceptors 20
TPSA 349.62 Ų
Rotatable bonds 2
Aromatic rings 4 / 7
Heavy atoms 46
Fraction sp³ C 0.50
Formula C20H24N10O14P2

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 690.4
  • LogP ≤ 5 -3.05
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 349.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O)(O[C@@H]5[C@@H](CO[P@@](=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
InChIKey 
PKFDLKSEZWEFGL-MHARETSRSA-N

Provenance

Annotation context from LigQ_2 search.

Method
LigQ sequence
Source
PDB
Binding sites
PF07238

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3542.

ZINC 50

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

Compound Similarity (Tanimoto)