Ligand profile

RBT

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

Bound to: KP13_03630 — Acriflavine resistance protein B

Via homolog PDB 6zo9 UniProt P31224 Formula C₄₆H₆₂N₄O₁₁
Mol. weight 847.02 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
RBT
PDB
6zo9
UniProt (similar protein)
P31224
Target protein
KP13_03630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 847.02 Da
LogP (Crippen) 4.62
H-bond donors 5
H-bond acceptors 14
TPSA 205.55 Ų
Rotatable bonds 4
Aromatic rings 1 / 6
Heavy atoms 61
Fraction sp³ C 0.59
Formula C₄₆H₆₂N₄O₁₁

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 205.5
  • −1 ≤ LogP ≤ 5 4.62
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 847.0
  • LogP ≤ 5 4.62
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 205.5
PAINS Alert

Matches PAINS filter: quinone_A(370). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](\C=C\C=C(/C(=O)NC(=C5C3=NC6(N5)CCN(CC6)CC(C)C)C2=O)\C)C)O)C)O)C)OC(=O)C)C)OC)C)O
InChI 
InChI=1S/C46H62N4O11/c1-22(2)21-50-18-16-46(17-19-50)48-34-31-32-39(54)28(8)42-33(31)43(56)45(10,61-42)59-20-15-30(58-11)25(5)41(60-29(9)51)27(7)38(53)26(6)37(52)23(3)13-12-14-24(4)44(57)47-36(40(32)55)35(34)49-46/h12-15,20,22-23,25-27,30,37-38,41,49,52-54H,16-19,21H2,1-11H3,(H,47,57)/b13-12+,20-15+,24-14-/t23-,25+,26+,27+,30-,37-,38+,41+,45-/m0/s1
InChIKey 
ATEBXHFBFRCZMA-VXTBVIBXSA-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
PF00873

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_03630.

PDB 33

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

Ligand PDB entry

ChEMBL 53

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)