Binder profile

APC

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

Bound to: PA4663 — molybdopterin biosynthesis protein MoeB

Via homolog PDB 3h9j UniProt Q47506 C11H18N5O12P3
Mol. weight 505.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
APC
PDB
3h9j
UniProt (similar protein)
Q47506
Target protein
PA4663

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 505.21 Da
LogP (Crippen) -1.52
H-bond donors 7
H-bond acceptors 13
TPSA 269.90 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.55
Formula C11H18N5O12P3

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 3 violations
  • MW ≤ 500 Da 505.2
  • LogP ≤ 5 -1.52
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 269.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
InChI 
InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKey 
CAWZRIXWFRFUQB-IOSLPCCCSA-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
PF00899

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA4663.

PDB 3

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

Ligand PDB entry

ChEMBL 30

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)