Binder profile

K3E

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

Bound to: PA3088 — NAD kinase

Via homolog PDB 6rga UniProt Q8Y8D7 C23H27N11O7
Mol. weight 569.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K3E
PDB
6rga
UniProt (similar protein)
Q8Y8D7
Target protein
PA3088

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 569.54 Da
LogP (Crippen) -3.60
H-bond donors 7
H-bond acceptors 18
TPSA 273.87 Ų
Rotatable bonds 6
Aromatic rings 4 / 6
Heavy atoms 41
Fraction sp³ C 0.48
Formula C23H27N11O7

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 569.5
  • LogP ≤ 5 -3.60
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 273.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COCC#Cc4nc5c(ncnc5n4C6C(C(C(O6)CN)O)O)N)O)O)N
InChI 
InChI=1S/C23H27N11O7/c24-4-9-14(35)17(38)23(40-9)34-11(32-13-19(26)28-7-30-21(13)34)2-1-3-39-5-10-15(36)16(37)22(41-10)33-8-31-12-18(25)27-6-29-20(12)33/h6-10,14-17,22-23,35-38H,3-5,24H2,(H2,25,27,29)(H2,26,28,30)
InChIKey 
NNTKMVAYMCZJCQ-UHFFFAOYSA-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)