Ligand profile

PRT

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

Bound to: KP13_03767 — ATP phosphoribosyltransferase

Via homolog PDB 1q1k UniProt P60757 Formula C₁₅H₂₅N₅O₂₀P₄
Mol. weight 719.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PRT
PDB
1q1k
UniProt (similar protein)
P60757
Target protein
KP13_03767

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 719.28 Da
LogP (Crippen) -3.60
H-bond donors 11
H-bond acceptors 19
TPSA 385.45 Ų
Rotatable bonds 12
Aromatic rings 2 / 4
Heavy atoms 44
Fraction sp³ C 0.67
Formula C₁₅H₂₅N₅O₂₀P₄

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 385.5
  • −1 ≤ LogP ≤ 5 -3.60
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 719.3
  • LogP ≤ 5 -3.60
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 385.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C\1/c2c(n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=CN1[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O
InChI 
InChI=1S/C15H25N5O20P4/c16-12-7-13(18-4-19(12)14-10(23)8(21)5(37-14)1-35-41(25,26)27)20(3-17-7)15-11(24)9(22)6(38-15)2-36-43(31,32)40-44(33,34)39-42(28,29)30/h3-6,8-11,14-16,21-24H,1-2H2,(H,31,32)(H,33,34)(H2,25,26,27)(H2,28,29,30)/b16-12-/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
InChIKey 
RKNHJBVBFHDXGR-DNVSJNHSSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF01634

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_03767.

PDB 3

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)