Ligand profile

CC5

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

Bound to: KP13_02430 — putative inorganic polyphosphate/ATP-NAD kinase

Via homolog PDB 2i2b UniProt Q8Y8D7 Formula C₉H₁₁N₅O₃
Mol. weight 237.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CC5
PDB
2i2b
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 237.22 Da
LogP (Crippen) -1.34
H-bond donors 3
H-bond acceptors 8
TPSA 119.31 Ų
Rotatable bonds 1
Aromatic rings 2 / 3
Heavy atoms 17
Fraction sp³ C 0.44
Formula C₉H₁₁N₅O₃

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 119.3
  • −1 ≤ LogP ≤ 5 -1.34
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 237.2
  • LogP ≤ 5 -1.34
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 119.3
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](CO3)O)O)N
InChI 
InChI=1S/C9H11N5O3/c10-7-5-8(12-2-11-7)14(3-13-5)9-6(16)4(15)1-17-9/h2-4,6,9,15-16H,1H2,(H2,10,11,12)/t4-,6-,9-/m1/s1
InChIKey 
DTGVOXMKTYPSSO-NVMQTXNBSA-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
PF01513' 'PF20143

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_02430.

PDB 51

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

Ligand PDB entry

ChEMBL 3

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)