Binder profile

FD5

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

Bound to: PA1962 — FMN-dependent NADH-azoreductase

Via homolog PDB 4c14 UniProt Q88IY3 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
PA1962

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.

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 TPW 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 binders for this protein

Quick navigation to other ligands bound to PA1962.

PDB 8

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)