Ligand profile

NYZ

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

Bound to: KP13_03610 — Bifunctional protein UshA

Via homolog PDB 6tw0 UniProt P21589 Formula C₁₁H₁₇N₅O₁₀P₂
Mol. weight 441.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NYZ
PDB
6tw0
UniProt (similar protein)
P21589
Target protein
KP13_03610

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 441.23 Da
LogP (Crippen) -2.34
H-bond donors 7
H-bond acceptors 11
TPSA 243.34 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 28
Fraction sp³ C 0.55
Formula C₁₁H₁₇N₅O₁₀P₂

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 243.3
  • −1 ≤ LogP ≤ 5 -2.34
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 441.2
  • LogP ≤ 5 -2.34
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 243.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(CP(=O)(O)O)O)O)O)NC(=O)N=C2N
InChI 
InChI=1S/C11H17N5O10P2/c12-8-5-9(15-11(19)14-8)16(2-13-5)10-7(18)6(17)4(26-10)1-25-28(23,24)3-27(20,21)22/h2,4,6-7,10,17-18H,1,3H2,(H,23,24)(H2,20,21,22)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1
InChIKey 
ZFKXMQLZXNYUBT-KQYNXXCUSA-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
PF00149' 'PF02872

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_03610.

PDB 14

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

Ligand PDB entry

ChEMBL 100

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)