Ligand profile

NHD

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

Bound to: VK055_2536 — dihydrodipicolinate reductase

Via homolog PDB 1drw UniProt P04036 Formula C₂₁H₂₆N₆O₁₅P₂
Mol. weight 664.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NHD
PDB
1drw
UniProt (similar protein)
P04036
Target protein
VK055_2536

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 664.41 Da
LogP (Crippen) -3.52
H-bond donors 7
H-bond acceptors 18
TPSA 315.30 Ų
Rotatable bonds 11
Aromatic rings 3 / 5
Heavy atoms 44
Fraction sp³ C 0.48
Formula C₂₁H₂₆N₆O₁₅P₂

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 315.3
  • −1 ≤ LogP ≤ 5 -3.52
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 664.4
  • LogP ≤ 5 -3.52
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 315.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5O)O)O)O)O)C(=O)N
InChI 
InChI=1S/C21H26N6O15P2/c22-17(32)9-2-1-3-26(4-9)20-15(30)13(28)10(40-20)5-38-43(34,35)42-44(36,37)39-6-11-14(29)16(31)21(41-11)27-8-25-12-18(27)23-7-24-19(12)33/h1-4,7-8,10-11,13-16,20-21,28-31H,5-6H2,(H4-,22,23,24,32,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKey 
DGVSIBCCYUVRNA-NNYOXOHSSA-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)