Ligand profile

KNG

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

Bound to: KP13_31791 — RNA polymerase sigma factor RpoD

Via homolog PDB 6cux UniProt P00579 Formula C₅₀H₆₇NO₁₉
Mol. weight 986.07 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
KNG
PDB
6cux
UniProt (similar protein)
P00579
Target protein
KP13_31791

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 986.07 Da
LogP (Crippen) 5.64
H-bond donors 7
H-bond acceptors 18
TPSA 292.60 Ų
Rotatable bonds 8
Aromatic rings 2 / 7
Heavy atoms 70
Fraction sp³ C 0.62
Formula C₅₀H₆₇NO₁₉

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 292.6
  • −1 ≤ LogP ≤ 5 5.64
Lipinski's Rule of Five Fail 4 violations
  • MW ≤ 500 Da 986.1
  • LogP ≤ 5 5.64
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 292.6
PAINS Alert

Matches PAINS filter: keto_naphthol_A(2). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c2c3c(cc(c2O)NC(=O)/C(=C\CC[C@@H]([C@@H]([C@H]([C@H]([C@H]([C@@H]([C@@H]([C@H](/C=C/O[C@@]4(C(=O)c3c1O4)C)O[C@H]5C[C@H]6[C@@H]([C@H](O5)C)OCO6)C)OC(=O)C)C)O)C)O)[C@H](C)OC(=O)C(C)(C)CC(=O)O)/C)O)O
InChI 
InChI=1S/C50H67NO19/c1-21-13-12-14-29(26(6)67-48(62)49(9,10)19-34(54)55)40(57)23(3)39(56)24(4)43(68-28(8)52)22(2)32(69-35-18-33-45(27(7)66-35)64-20-63-33)15-16-65-50(11)46(60)38-36-31(53)17-30(51-47(21)61)42(59)37(36)41(58)25(5)44(38)70-50/h13,15-17,22-24,26-27,29,32-33,35,39-40,43,45,53,56-59H,12,14,18-20H2,1-11H3,(H,51,61)(H,54,55)/b16-15+,21-13-/t22-,23+,24-,26+,27-,29-,32+,33+,35+,39-,40-,43-,45-,50+/m1/s1
InChIKey 
RKRZBNCHQZDJPK-UAXKWEMASA-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
PF04563' 'PF04565

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_31791.

PDB 12

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)