Ligand profile

5DL

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

Bound to: KP13_03770 — Histidine biosynthesis bifunctional protein

Via homolog PDB 5ekw UniProt O23346 Formula C₅H₁₀N₃O₄P
Mol. weight 207.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5DL
PDB
5ekw
UniProt (similar protein)
O23346
Target protein
KP13_03770

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 207.13 Da
LogP (Crippen) -1.18
H-bond donors 3
H-bond acceptors 5
TPSA 108.47 Ų
Rotatable bonds 4
Aromatic rings 1 / 1
Heavy atoms 13
Fraction sp³ C 0.60
Formula C₅H₁₀N₃O₄P

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 108.5
  • −1 ≤ LogP ≤ 5 -1.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 207.1
  • LogP ≤ 5 -1.18
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 108.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ncn(n1)C[C@@H](CP(=O)(O)O)O
InChI 
InChI=1S/C5H10N3O4P/c9-5(2-13(10,11)12)1-8-4-6-3-7-8/h3-5,9H,1-2H2,(H2,10,11,12)/t5-/m0/s1
InChIKey 
ZXKJPBBOMRHTCH-YFKPBYRVSA-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
PF00475

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_03770.

PDB 4

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

Ligand PDB entry

ChEMBL 15

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 34

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)