Ligand profile

B6P

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

Bound to: KP13_00525 — ribokinase-like superfamily protein

Via homolog PDB 3rqh UniProt P94368 Formula C₂₀H₃₀N₁₀O₂₅P₆
Mol. weight 996.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B6P
PDB
3rqh
UniProt (similar protein)
P94368
Target protein
KP13_00525

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 996.35 Da
LogP (Crippen) -2.21
H-bond donors 12
H-bond acceptors 29
TPSA 527.03 Ų
Rotatable bonds 18
Aromatic rings 4 / 6
Heavy atoms 61
Fraction sp³ C 0.50
Formula C₂₀H₃₀N₁₀O₂₅P₆

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 527.0
  • −1 ≤ LogP ≤ 5 -2.21
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 996.3
  • LogP ≤ 5 -2.21
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 29
Veber's rules Fail
  • Rotatable bonds ≤ 10 18
  • TPSA ≤ 140 Ų 527.0
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)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N
InChI 
InChI=1S/C20H30N10O25P6/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(49-19)1-47-56(35,36)51-58(39,40)53-60(43,44)55-61(45,46)54-59(41,42)52-57(37,38)48-2-8-12(32)14(34)20(50-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H,43,44)(H,45,46)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKey 
PZCFFCOJNXGTIM-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
PF01256

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_00525.

PDB 9

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)