Ligand profile

2B9

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

Bound to: VK055_1732 — adenosylmethionine-8-amino-7-oxononanoate transaminase

Via homolog PDB 4mqr UniProt P9WQ81 Formula C₁₄H₁₅N₄O₆P
Mol. weight 366.27 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
2B9
PDB
4mqr
UniProt (similar protein)
P9WQ81
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 366.27 Da
LogP (Crippen) 1.94
H-bond donors 4
H-bond acceptors 7
TPSA 153.70 Ų
Rotatable bonds 5
Aromatic rings 1 / 2
Heavy atoms 25
Fraction sp³ C 0.14
Formula C₁₄H₁₅N₄O₆P

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 153.7
  • −1 ≤ LogP ≤ 5 1.94
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 366.3
  • LogP ≤ 5 1.94
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 153.7
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=C(/C(=C\N=N\C(=O)c2ccncc2)/C(=CN1)COP(=O)(O)O)O
InChI 
InChI=1S/C14H15N4O6P/c1-9-13(19)12(11(6-16-9)8-24-25(21,22)23)7-17-18-14(20)10-2-4-15-5-3-10/h2-7,16,19H,8H2,1H3,(H2,21,22,23)/b12-7-,18-17+
InChIKey 
GXGBRTHJGGLQAZ-UMMCPOKDSA-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
PF00202

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_1732.

PDB 25

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

Ligand PDB entry

ChEMBL 100

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

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)