Binder profile

ZINC4778021

Virtual-screening candidate from ZINC.

Bound to: PA3088 — NAD kinase

Via homolog UniProt Q8Y8D7 C12H17N5O
Tanimoto 0.66
Mol. weight 247.30 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4778021
UniProt (similar protein)
Q8Y8D7
Tanimoto
0.659
Target protein
PA3088

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 247.30 Da
LogP (Crippen) 1.59
H-bond donors 0
H-bond acceptors 6
TPSA 56.07 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 18
Fraction sp³ C 0.58
Formula C12H17N5O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 247.3
  • LogP ≤ 5 1.59
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 56.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)c1ncnc2c1ncn2[C@@H]1CCCCO1
InChI 
InChI=1S/C12H17N5O/c1-16(2)11-10-12(14-7-13-11)17(8-15-10)9-5-3-4-6-18-9/h7-9H,3-6H2,1-2H3/t9-/m0/s1
InChIKey 
VZGMVQPZSLXUDB-VIFPVBQESA-N

Provenance

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

Method
LigQ nearest_k
Query
KF5
Homolog
Q8Y8D7

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 52

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 49

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

Compound Similarity (Tanimoto)