Ligand profile

A12

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

Bound to: KP13_00004 — Ribokinase

Via homolog PDB 6wjz UniProt Q9H477 Formula C₁₁H₁₇N₅O₉P₂
Mol. weight 425.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A12
PDB
6wjz
UniProt (similar protein)
Q9H477
Target protein
KP13_00004

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 425.23 Da
LogP (Crippen) -1.64
H-bond donors 6
H-bond acceptors 11
TPSA 223.37 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 27
Fraction sp³ C 0.55
Formula C₁₁H₁₇N₅O₉P₂

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 223.4
  • −1 ≤ LogP ≤ 5 -1.64
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 425.2
  • LogP ≤ 5 -1.64
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 223.4
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)(CP(=O)(O)O)O)O)O)N
InChI 
InChI=1S/C11H17N5O9P2/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(25-11)1-24-27(22,23)4-26(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKey 
OLCWZBFDIYXLAA-IOSLPCCCSA-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
PF00294

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_00004.

PDB 5

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)