Ligand profile

NAX

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

Bound to: KP13_00525 — ribokinase-like superfamily protein

Via homolog PDB 3rq2 UniProt P94368 Formula C₂₁H₃₁N₇O₁₅P₂
Mol. weight 683.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NAX
PDB
3rq2
UniProt (similar protein)
P94368
Target protein
KP13_00525

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 683.46 Da
LogP (Crippen) -3.49
H-bond donors 9
H-bond acceptors 19
TPSA 337.85 Ų
Rotatable bonds 11
Aromatic rings 2 / 5
Heavy atoms 45
Fraction sp³ C 0.62
Formula C₂₁H₃₁N₇O₁₅P₂

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 337.8
  • −1 ≤ LogP ≤ 5 -3.49
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 683.5
  • LogP ≤ 5 -3.49
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 337.8
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)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=C(CC[C@@H]5O)C(=O)N)O)O)O)O)N
InChI 
InChI=1S/C21H31N7O15P2/c22-17-12-19(25-6-24-17)28(7-26-12)21-16(33)14(31)10(42-21)5-40-45(37,38)43-44(35,36)39-4-9-13(30)15(32)20(41-9)27-3-8(18(23)34)1-2-11(27)29/h3,6-7,9-11,13-16,20-21,29-33H,1-2,4-5H2,(H2,23,34)(H,35,36)(H,37,38)(H2,22,24,25)/t9-,10-,11+,13-,14-,15-,16-,20-,21-/m1/s1
InChIKey 
IDBZKGQRLBFUFQ-VPHRTNKSSA-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
PF01256

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_00525.

PDB 9

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)