Binder profile

GAV

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

Bound to: PA4843 — two-component response regulator

Via homolog PDB 2v0n UniProt B8GZM2 C10H16N5O13P3S
Mol. weight 539.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GAV
PDB
2v0n
UniProt (similar protein)
B8GZM2
Target protein
PA4843

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 539.25 Da
LogP (Crippen) -1.40
H-bond donors 8
H-bond acceptors 14
TPSA 278.87 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.50
Formula C10H16N5O13P3S

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 539.2
  • LogP ≤ 5 -1.40
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 278.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O[P@@](=O)(O)OP(=O)(O)O)S)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-31(24,32)28-30(22,23)27-29(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,32)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-,31-/m1/s1
InChIKey 
YRUWXBKVSXSSGS-KIOICMOXSA-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
PF00990

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA4843.

PDB 3

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)