Ligand profile

P9D

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

Bound to: KP13_03630 — Acriflavine resistance protein B

Via homolog PDB 3w9h UniProt P31224 Formula C₃₁H₃₉N₁₁O₆S
Mol. weight 693.79 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P9D
PDB
3w9h
UniProt (similar protein)
P31224
Target protein
KP13_03630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 693.79 Da
LogP (Crippen) 0.91
H-bond donors 3
H-bond acceptors 14
TPSA 212.52 Ų
Rotatable bonds 11
Aromatic rings 4 / 5
Heavy atoms 49
Fraction sp³ C 0.45
Formula C₃₁H₃₉N₁₁O₆S

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 212.5
  • −1 ≤ LogP ≤ 5 0.91
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 693.8
  • LogP ≤ 5 0.91
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 212.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)c1csc(n1)NC(=O)C2=CC3=NC(=C(C(=O)N3C=C2)/C=C/c4[nH]nnn4)N5CCC[C@H](C5)OC(=O)NCC[N+](C)(C)CC(=O)[O-]
InChI 
InChI=1S/C31H39N11O6S/c1-31(2,3)22-18-49-29(33-22)35-27(45)19-10-13-41-24(15-19)34-26(21(28(41)46)8-9-23-36-38-39-37-23)40-12-6-7-20(16-40)48-30(47)32-11-14-42(4,5)17-25(43)44/h8-10,13,15,18,20H,6-7,11-12,14,16-17H2,1-5H3,(H3-,32,33,35,36,37,38,39,43,44,45,47)/t20-/m1/s1
InChIKey 
RVJNIKFVEAWLQC-HXUWFJFHSA-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)