Ligand profile

K3E

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

Bound to: KP13_02430 — putative inorganic polyphosphate/ATP-NAD kinase

Via homolog PDB 6rga UniProt Q8Y8D7 Formula 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
KP13_02430

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.

  • TPSA ≤ 90 Ų 273.9
  • −1 ≤ LogP ≤ 5 -3.60
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 Target 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 ligands for this protein

Quick navigation to other ligands bound to KP13_02430.

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)