Ligand profile

T5K

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

Bound to: KP13_01696 — Lipopolysaccharide biosynthesis protein rffA

Via homolog PDB 4zah UniProt P27833 Formula C₂₄H₃₅N₄O₁₉P₃
Mol. weight 776.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
T5K
PDB
4zah
UniProt (similar protein)
P27833
Target protein
KP13_01696

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 776.48 Da
LogP (Crippen) -1.28
H-bond donors 9
H-bond acceptors 18
TPSA 348.54 Ų
Rotatable bonds 13
Aromatic rings 2 / 4
Heavy atoms 50
Fraction sp³ C 0.58
Formula C₂₄H₃₅N₄O₁₉P₃

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 348.5
  • −1 ≤ LogP ≤ 5 -1.28
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 776.5
  • LogP ≤ 5 -1.28
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 348.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H](C[C@@H](O3)N4C=C(C(=O)NC4=O)C)O)C)O
InChI 
InChI=1S/C24H35N4O19P3/c1-10-7-28(24(34)27-22(10)33)17-4-15(29)16(45-17)9-43-49(38,39)47-50(40,41)46-23-21(32)20(31)18(12(3)44-23)26-6-14-13(8-42-48(35,36)37)5-25-11(2)19(14)30/h5-7,12,15-18,20-21,23,29-32H,4,8-9H2,1-3H3,(H,38,39)(H,40,41)(H,27,33,34)(H2,35,36,37)/b26-6+/t12-,15+,16-,17-,18+,20+,21-,23-/m1/s1
InChIKey 
LEIRFGMKEVPNBT-QBLVGKJYSA-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
PF01041

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_01696.

PDB 7

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)