Ligand profile

A3D

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

Bound to: VK055_2536 — dihydrodipicolinate reductase

Via homolog PDB 1drv UniProt P04036 Formula C₂₂H₂₈N₆O₁₄P₂
Mol. weight 662.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A3D
PDB
1drv
UniProt (similar protein)
P04036
Target protein
VK055_2536

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 662.44 Da
LogP (Crippen) -2.54
H-bond donors 6
H-bond acceptors 18
TPSA 295.07 Ų
Rotatable bonds 11
Aromatic rings 3 / 5
Heavy atoms 44
Fraction sp³ C 0.50
Formula C₂₂H₂₈N₆O₁₄P₂

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 295.1
  • −1 ≤ LogP ≤ 5 -2.54
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 662.4
  • LogP ≤ 5 -2.54
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 295.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)c1ccc[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O
InChI 
InChI=1S/C22H28N6O14P2/c1-10(29)11-3-2-4-27(5-11)21-17(32)15(30)12(40-21)6-38-43(34,35)42-44(36,37)39-7-13-16(31)18(33)22(41-13)28-9-26-14-19(23)24-8-25-20(14)28/h2-5,8-9,12-13,15-18,21-22,30-33H,6-7H2,1H3,(H3-,23,24,25,34,35,36,37)/t12-,13-,15-,16-,17-,18-,21-,22-/m1/s1
InChIKey 
KPVQNXLUPNWQHM-RBEMOOQDSA-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
PF01113' 'PF05173

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_2536.

PDB 7

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)