Ligand profile

12D

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

Bound to: KP13_05549 — ABC transporter domain-containing protein

Via homolog PDB 3b5j UniProt P08716 Formula C₁₆H₁₆N₈O₁₆P₂
Mol. weight 638.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
12D
PDB
3b5j
UniProt (similar protein)
P08716
Target protein
KP13_05549

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 638.29 Da
LogP (Crippen) -1.01
H-bond donors 4
H-bond acceptors 18
TPSA 340.02 Ų
Rotatable bonds 9
Aromatic rings 2 / 5
Heavy atoms 42
Fraction sp³ C 0.44
Formula C₁₆H₁₆N₈O₁₆P₂

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 340.0
  • −1 ≤ LogP ≤ 5 -1.01
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 638.3
  • LogP ≤ 5 -1.01
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 340.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@H]4[C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[C@@]5(O4)[C@@H](C=C(C=C5[N+](=O)[O-])[N+](=O)[O-])[N+](=O)[O-])N
InChI 
InChI=1S/C16H16N8O16P2/c17-13-10-14(19-4-18-13)21(5-20-10)15-12-11(7(37-15)3-36-42(34,35)40-41(31,32)33)38-16(39-12)8(23(27)28)1-6(22(25)26)2-9(16)24(29)30/h1-2,4-5,7-8,11-12,15H,3H2,(H,34,35)(H2,17,18,19)(H2,31,32,33)/t7-,8-,11-,12-,15-,16-/m1/s1
InChIKey 
WYOHYTDXVJMKHS-BENPRDFYSA-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
PF00005

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_05549.

PDB 6

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)