Ligand profile

6BM

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

Bound to: KP13_02390 — Enolase

Via homolog PDB 5idz UniProt P09104 Formula C₅H₁₀NO₅P
Mol. weight 195.11 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6BM
PDB
5idz
UniProt (similar protein)
P09104
Target protein
KP13_02390

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 195.11 Da
LogP (Crippen) -0.46
H-bond donors 3
H-bond acceptors 3
TPSA 98.07 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 12
Fraction sp³ C 0.80
Formula C₅H₁₀NO₅P

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 98.1
  • −1 ≤ LogP ≤ 5 -0.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 195.1
  • LogP ≤ 5 -0.46
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 98.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1C[C@@H](C(=O)N(C1)O)P(=O)(O)O
InChI 
InChI=1S/C5H10NO5P/c7-5-4(12(9,10)11)2-1-3-6(5)8/h4,8H,1-3H2,(H2,9,10,11)/t4-/m0/s1
InChIKey 
DVZQUMSQEGOYMX-BYPYZUCNSA-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
PF00113' 'PF03952

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_02390.

PDB 9

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

Ligand PDB entry

ZINC 35

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

Compound Similarity (Tanimoto)