Ligand profile

5A9

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

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

Via homolog PDB 5dht UniProt Q8Y8D7 Formula C₂₀H₂₂BrN₉O₄S
Mol. weight 564.43 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
5A9
PDB
5dht
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 564.43 Da
LogP (Crippen) 1.55
H-bond donors 4
H-bond acceptors 11
TPSA 197.17 Ų
Rotatable bonds 9
Aromatic rings 3 / 4
Heavy atoms 35
Fraction sp³ C 0.40
Formula C₂₀H₂₂BrN₉O₄S

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 197.2
  • −1 ≤ LogP ≤ 5 1.55
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 564.4
  • LogP ≤ 5 1.55
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 197.2
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

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)CN=[N+]=[N-])O)O)N
InChI 
InChI=1S/C20H22BrN9O4S/c21-11-3-1-2-10(6-11)4-5-24-13(31)8-35-20-28-14-17(22)25-9-26-18(14)30(20)19-16(33)15(32)12(34-19)7-27-29-23/h1-3,6,9,12,15-16,19,32-33H,4-5,7-8H2,(H,24,31)(H2,22,25,26)/t12-,15-,16-,19-/m1/s1
InChIKey 
JYGMOYIMZQWVHO-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)