Ligand profile

5AK

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

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

Via homolog PDB 5dhq UniProt Q8Y8D7 Formula C₂₀H₂₃BrN₆O₅S
Mol. weight 539.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5AK
PDB
5dhq
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 539.41 Da
LogP (Crippen) 0.23
H-bond donors 5
H-bond acceptors 11
TPSA 168.64 Ų
Rotatable bonds 8
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.40
Formula C₂₀H₂₃BrN₆O₅S

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 168.6
  • −1 ≤ LogP ≤ 5 0.23
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 539.4
  • LogP ≤ 5 0.23
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 168.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)Br)CCNC(=O)CSc2nc3c(ncnc3n2[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O)N
InChI 
InChI=1S/C20H23BrN6O5S/c21-11-3-1-2-10(6-11)4-5-23-13(29)8-33-20-26-14-17(22)24-9-25-18(14)27(20)19-16(31)15(30)12(7-28)32-19/h1-3,6,9,12,15-16,19,28,30-31H,4-5,7-8H2,(H,23,29)(H2,22,24,25)/t12-,15-,16-,19-/m1/s1
InChIKey 
WJGLUXUMEHFNOZ-BGIGGGFGSA-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
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)