Ligand profile

NMN

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

Bound to: KP13_03557 — DNA ligase

Via homolog PDB 6kdu UniProt P9WNV1 Formula C₁₁H₁₆N₂O₈P⁺
Mol. weight 335.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NMN
PDB
6kdu
UniProt (similar protein)
P9WNV1
Target protein
KP13_03557

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 335.23 Da
LogP (Crippen) -2.20
H-bond donors 5
H-bond acceptors 6
TPSA 163.42 Ų
Rotatable bonds 5
Aromatic rings 1 / 2
Heavy atoms 22
Fraction sp³ C 0.45
Formula C₁₁H₁₆N₂O₈P⁺

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 163.4
  • −1 ≤ LogP ≤ 5 -2.20
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 335.2
  • LogP ≤ 5 -2.20
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 163.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C(=O)N
InChI 
InChI=1S/C11H15N2O8P/c12-10(16)6-2-1-3-13(4-6)11-9(15)8(14)7(21-11)5-20-22(17,18)19/h1-4,7-9,11,14-15H,5H2,(H3-,12,16,17,18,19)/p+1/t7-,8-,9-,11-/m1/s1
InChIKey 
DAYLJWODMCOQEW-TURQNECASA-O

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
PF22745

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)