Ligand profile

K3B

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

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

Via homolog PDB 6rg6 UniProt Q8Y8D7 Formula C₁₈H₁₈N₁₀O₄
Mol. weight 438.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K3B
PDB
6rg6
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 438.41 Da
LogP (Crippen) -1.66
H-bond donors 5
H-bond acceptors 13
TPSA 209.02 Ų
Rotatable bonds 4
Aromatic rings 4 / 5
Heavy atoms 32
Fraction sp³ C 0.33
Formula C₁₈H₁₈N₁₀O₄

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 209.0
  • −1 ≤ LogP ≤ 5 -1.66
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 438.4
  • LogP ≤ 5 -1.66
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 209.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)[nH]c(n2)C#CCOCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N
InChI 
InChI=1S/C18H18N10O4/c19-14-10-16(23-5-21-14)27-9(26-10)2-1-3-31-4-8-12(29)13(30)18(32-8)28-7-25-11-15(20)22-6-24-17(11)28/h5-8,12-13,18,29-30H,3-4H2,(H2,20,22,24)(H3,19,21,23,26,27)
InChIKey 
BVXWUAMSMQSLCT-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' 'PF20143

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)