Ligand profile

HDV

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

Bound to: KP13_03062 — putative metal-dependent phosphohydrolase

Via homolog PDB 6dwd UniProt Q9Y3Z3 Formula C₁₁H₁₇FN₅O₁₂P₃
Mol. weight 523.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HDV
PDB
6dwd
UniProt (similar protein)
Q9Y3Z3
Target protein
KP13_03062

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 523.20 Da
LogP (Crippen) -0.34
H-bond donors 6
H-bond acceptors 13
TPSA 258.90 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.55
Formula C₁₁H₁₇FN₅O₁₂P₃

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 258.9
  • −1 ≤ LogP ≤ 5 -0.34
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 523.2
  • LogP ≤ 5 -0.34
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 258.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1nc(c2c(n1)n(cn2)[C@H]3[C@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F)N
InChI 
InChI=1S/C11H17FN5O12P3/c1-4-15-9(13)7-10(16-4)17(3-14-7)11-6(12)8(18)5(27-11)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3,5-6,8,11,18H,2H2,1H3,(H,22,23)(H,24,25)(H2,13,15,16)(H2,19,20,21)/t5-,6+,8-,11-/m1/s1
InChIKey 
BGNIGZFVXIGOQD-WCGPTHBMSA-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
PF01966

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_03062.

PDB 22

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

Ligand PDB entry

ChEMBL 1

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)