Binder profile

N7Y

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

Bound to: PA3108 — amidophosphoribosyltransferase

Via homolog PDB 6ott UniProt P0AG16 C10H17N5O16P4
Mol. weight 587.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
N7Y
PDB
6ott
UniProt (similar protein)
P0AG16
Target protein
PA3108

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 587.16 Da
LogP (Crippen) -1.51
H-bond donors 8
H-bond acceptors 15
TPSA 325.66 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 35
Fraction sp³ C 0.50
Formula C10H17N5O16P4

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 587.2
  • LogP ≤ 5 -1.51
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 325.7
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)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N
InChI 
InChI=1S/C10H17N5O16P4/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(29-35(25,26)31-33(20,21)22)4(28-10)1-27-34(23,24)30-32(17,18)19/h2-4,6-7,10,16H,1H2,(H,23,24)(H,25,26)(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
InChIKey 
DWZMGWMGGHNJLF-KQYNXXCUSA-N

Provenance

Annotation context from LigQ_2 search.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF13522

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3108.

PDB 9

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

Ligand PDB entry

ChEMBL 2

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)