Binder profile

5NB

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

Bound to: PA3088 — NAD kinase

Via homolog PDB 3v8n UniProt Q8Y8D7 C10H13BrN6O3
Mol. weight 345.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5NB
PDB
3v8n
UniProt (similar protein)
Q8Y8D7
Target protein
PA3088

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 345.16 Da
LogP (Crippen) -1.25
H-bond donors 4
H-bond acceptors 9
TPSA 145.33 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.50
Formula C10H13BrN6O3

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 Pass 0 violations
  • MW ≤ 500 Da 345.2
  • LogP ≤ 5 -1.25
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 145.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(c(n2)Br)[C@H]3[C@@H]([C@@H]([C@H](O3)CN)O)O)N
InChI 
InChI=1S/C10H13BrN6O3/c11-10-16-4-7(13)14-2-15-8(4)17(10)9-6(19)5(18)3(1-12)20-9/h2-3,5-6,9,18-19H,1,12H2,(H2,13,14,15)/t3-,5-,6-,9-/m1/s1
InChIKey 
WSWAKFOKHOTDLO-UUOKFMHZSA-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
PF01513

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3088.

PDB 51

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

Ligand PDB entry

ChEMBL 3

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)