Ligand profile

IVH

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

Bound to: KP13_03557 — DNA ligase

Via homolog PDB 3pn1 UniProt P43813 Formula C₁₄H₂₁N₅O₄S
Mol. weight 355.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
IVH
PDB
3pn1
UniProt (similar protein)
P43813
Target protein
KP13_03557

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 355.42 Da
LogP (Crippen) -0.09
H-bond donors 4
H-bond acceptors 10
TPSA 139.54 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.64
Formula C₁₄H₂₁N₅O₄S

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 139.5
  • −1 ≤ LogP ≤ 5 -0.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 355.4
  • LogP ≤ 5 -0.09
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 139.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCSc1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N
InChI 
InChI=1S/C14H21N5O4S/c1-2-3-4-24-14-17-11(15)8-12(18-14)19(6-16-8)13-10(22)9(21)7(5-20)23-13/h6-7,9-10,13,20-22H,2-5H2,1H3,(H2,15,17,18)/t7-,9-,10-,13-/m1/s1
InChIKey 
JUZWTKSKLZRPBL-QYVSTXNMSA-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
PF01653

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_03557.

PDB 8

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

Ligand PDB entry

ChEMBL 1

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)