Ligand profile

FD5

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

Bound to: KP13_04981 — FMN-dependent NADH-azoreductase

Via homolog PDB 4c14 UniProt Q88IY3 Formula C₄₂H₅₄N₉O₂₁PS₄
Mol. weight 1180.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FD5
PDB
4c14
UniProt (similar protein)
Q88IY3
Target protein
KP13_04981

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1180.18 Da
LogP (Crippen) 5.33
H-bond donors 21
H-bond acceptors 28
TPSA 503.13 Ų
Rotatable bonds 21
Aromatic rings 5 / 7
Heavy atoms 77
Fraction sp³ C 0.24
Formula C₄₂H₅₄N₉O₂₁PS₄

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 503.1
  • −1 ≤ LogP ≤ 5 5.33
Lipinski's Rule of Five Fail 4 violations
  • MW ≤ 500 Da 1180.2
  • LogP ≤ 5 5.33
  • H-bond donors ≤ 5 21
  • H-bond acceptors ≤ 10 28
Veber's rules Fail
  • Rotatable bonds ≤ 10 21
  • TPSA ≤ 140 Ų 503.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(cc1C)N(C3=NC(=O)N(C(=O)C3=N2)OCCS(c4ccc(cc4)NNc5c(cc6cc(c(c(c6c5N)O)NNc7ccc(cc7)S(C)(O)O)S(O)(O)O)S(O)(O)O)(O)O)CC(C(C(COP(=O)(O)O)O)O)O
InChI 
InChI=1S/C42H54N9O21PS4/c1-20-14-27-28(15-21(20)2)50(18-29(52)38(54)30(53)19-72-73(58,59)60)40-37(44-27)41(56)51(42(57)45-40)71-12-13-75(63,64)26-10-6-24(7-11-26)46-48-35-31(76(65,66)67)16-22-17-32(77(68,69)70)36(39(55)33(22)34(35)43)49-47-23-4-8-25(9-5-23)74(3,61)62/h4-11,14-17,29-30,38,46-49,52-55,61-70H,12-13,18-19,43H2,1-3H3,(H2,58,59,60)
InChIKey 
AKEFIPOJAGFOPZ-UHFFFAOYSA-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
PF02525

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_04981.

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)