Ligand profile

A38

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

Bound to: KP13_32224 — DNA polymerase IV

Via homolog PDB 6vg6 UniProt Q97W02 Formula C₁₀H₁₄N₅O₇P
Mol. weight 347.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A38
PDB
6vg6
UniProt (similar protein)
Q97W02
Target protein
KP13_32224

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 347.22 Da
LogP (Crippen) -1.54
H-bond donors 5
H-bond acceptors 9
TPSA 185.81 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₀H₁₄N₅O₇P

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 185.8
  • −1 ≤ LogP ≤ 5 -1.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 347.2
  • LogP ≤ 5 -1.54
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 185.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)N(C(=O)N2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
InChI 
InChI=1S/C10H14N5O7P/c11-8-7-9(13-3-12-8)15(10(17)14-7)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H,14,17)(H2,11,12,13)(H2,18,19,20)/t4-,5+,6+/m0/s1
InChIKey 
QFGWDFAYOAGQDH-KVQBGUIXSA-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
PF00817' 'PF11799

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_32224.

PDB 31

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)