Ligand profile

ZINC3869839

Virtual-screening candidate from ZINC.

Bound to: KP13_00955 — DNA gyrase subunit A

Via homolog UniProt Q99XG5 Formula C₁₀H₁₃N₅O₄
Tanimoto 0.75
Mol. weight 267.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3869839
UniProt (similar protein)
Q99XG5
Tanimoto
0.745
Target protein
KP13_00955

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 267.24 Da
LogP (Crippen) -1.66
H-bond donors 4
H-bond acceptors 8
TPSA 139.28 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.50
Formula C₁₀H₁₃N₅O₄

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 139.3
  • −1 ≤ LogP ≤ 5 -1.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 267.2
  • LogP ≤ 5 -1.66
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 139.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]1
InChI 
InChI=1S/C10H13N5O4/c11-10-13-8-7(9(18)14-10)12-3-15(8)6-1-4(17)5(2-16)19-6/h3-6,16-17H,1-2H2,(H3,11,13,14,18)/t4-,5-,6-/m0/s1
InChIKey 
YKBGVTZYEHREMT-ZLUOBGJFSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
DG
Homolog
Q99XG5

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_00955.

PDB 25

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 16

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)