Ligand profile

ZNB

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

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

Via homolog PDB 3v8p UniProt Q8Y8D7 Formula C₂₂H₂₅BrN₁₄O₇S
Mol. weight 709.50 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZNB
PDB
3v8p
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 709.50 Da
LogP (Crippen) -1.65
H-bond donors 7
H-bond acceptors 19
TPSA 316.48 Ų
Rotatable bonds 9
Aromatic rings 4 / 6
Heavy atoms 45
Fraction sp³ C 0.50
Formula C₂₂H₂₅BrN₁₄O₇S

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 316.5
  • −1 ≤ LogP ≤ 5 -1.65
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 709.5
  • LogP ≤ 5 -1.65
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 316.5
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 
c1nc(c2c(n1)n(c(n2)SCC(=O)NC[C@@H]3[C@H]([C@H]([C@@H](O3)n4c5c(c(ncn5)N)nc4Br)O)O)[C@H]6[C@@H]([C@@H]([C@H](O6)CN=[N+]=[N-])O)O)N
InChI 
InChI=1S/C22H25BrN14O7S/c23-21-33-9-15(24)28-4-30-17(9)36(21)19-13(41)11(39)6(43-19)1-27-8(38)3-45-22-34-10-16(25)29-5-31-18(10)37(22)20-14(42)12(40)7(44-20)2-32-35-26/h4-7,11-14,19-20,39-42H,1-3H2,(H,27,38)(H2,24,28,30)(H2,25,29,31)/t6-,7-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKey 
WFFKQQMGOXMIGR-ZOUOOXKVSA-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)