Ligand profile

38V

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

Bound to: KP13_04789 — hypothetical protein

Via homolog PDB 4ty0 UniProt Q9KVG7 Formula C₂₁H₃₀N₁₀O₁₉P₄
Mol. weight 850.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
38V
PDB
4ty0
UniProt (similar protein)
Q9KVG7
Target protein
KP13_04789

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 850.42 Da
LogP (Crippen) -3.04
H-bond donors 11
H-bond acceptors 23
TPSA 444.71 Ų
Rotatable bonds 14
Aromatic rings 4 / 6
Heavy atoms 54
Fraction sp³ C 0.52
Formula C₂₁H₃₀N₁₀O₁₉P₄

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 444.7
  • −1 ≤ LogP ≤ 5 -3.04
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 850.4
  • LogP ≤ 5 -3.04
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 23
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 444.7
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)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5NC(=NC6=O)N)O)O)O)N
InChI 
InChI=1S/C21H30N10O19P4/c22-15-9-16(25-3-24-15)30(4-26-9)20-13(34)14(8(48-20)2-45-51(36,37)6-52(38,39)50-53(40,41)42)49-54(43,44)46-1-7-11(32)12(33)19(47-7)31-5-27-10-17(31)28-21(23)29-18(10)35/h3-5,7-8,11-14,19-20,32-34H,1-2,6H2,(H,36,37)(H,38,39)(H,43,44)(H2,22,24,25)(H2,40,41,42)(H3,23,28,29,35)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKey 
QFHKDAVOJDVDDK-XPWFQUROSA-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
PF21654' 'PF21713

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_04789.

PDB 4

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)