Binder profile

CHEMBL5419012

Bioactivity hit from ChEMBL on a similar protein.

Bound to: PA3088 — NAD kinase

Via homolog UniProt Q721J8 C28H33N13O8
pchembl 6.30
Mol. weight 679.66 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5419012
UniProt (similar protein)
Q721J8
pchembl
6.300
Target protein
PA3088

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 679.66 Da
LogP (Crippen) -4.64
H-bond donors 8
H-bond acceptors 19
TPSA 300.06 Ų
Rotatable bonds 3
Aromatic rings 4 / 7
Heavy atoms 49
Fraction sp³ C 0.50
Formula C28H33N13O8

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 679.7
  • LogP ≤ 5 -4.64
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 300.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CN2CC#Cc3nc4c(N)ncnc4n3[C@@H]3O[C@H](CNC(=O)CCNC(=O)C2)[C@@H](O)[C@H]3O)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C28H33N13O8/c29-23-17-25(35-9-33-23)40(11-37-17)27-21(46)20(45)13(49-27)7-39-5-1-2-14-38-18-24(30)34-10-36-26(18)41(14)28-22(47)19(44)12(48-28)6-32-15(42)3-4-31-16(43)8-39/h9-13,19-22,27-28,44-47H,3-8H2,(H,31,43)(H,32,42)(H2,29,33,35)(H2,30,34,36)/t12-,13-,19-,20-,21-,22-,27-,28-/m1/s1
InChIKey 
VNLJLUGLNRIXOB-QJYUSYPVSA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF01513' 'PF20143

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 2

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)