Ligand profile

D5M

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

Bound to: KP13_00998 — hypothetical protein

Via homolog PDB 2pau UniProt P76491 Formula C₁₀H₁₄N₅O₆P
Mol. weight 331.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D5M
PDB
2pau
UniProt (similar protein)
P76491
Target protein
KP13_00998

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 331.23 Da
LogP (Crippen) -0.83
H-bond donors 4
H-bond acceptors 9
TPSA 165.84 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 22
Fraction sp³ C 0.50
Formula C₁₀H₁₄N₅O₆P

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 165.8
  • −1 ≤ LogP ≤ 5 -0.83
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 331.2
  • LogP ≤ 5 -0.83
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 165.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
InChI 
InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKey 
KHWCHTKSEGGWEX-RRKCRQDMSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF01966

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_00998.

PDB 4

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)