Ligand profile

MD1

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

Bound to: VK055_0600 — respiratory nitrate reductase, gamma subunit

Via homolog PDB 1q16 UniProt P11350 Formula C₂₀H₂₆N₁₀O₁₃P₂S₂
Mol. weight 740.57 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MD1
PDB
1q16
UniProt (similar protein)
P11350
Target protein
VK055_0600

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 740.57 Da
LogP (Crippen) -2.13
H-bond donors 12
H-bond acceptors 21
TPSA 357.96 Ų
Rotatable bonds 11
Aromatic rings 3 / 5
Heavy atoms 47
Fraction sp³ C 0.40
Formula C₂₀H₂₆N₁₀O₁₃P₂S₂

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 358.0
  • −1 ≤ LogP ≤ 5 -2.13
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 740.6
  • LogP ≤ 5 -2.13
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 21
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 358.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@H](/C(=C(\[C@H]4C=NC5=C(N4)C(=O)NC(=N5)N)/S)/S)O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C20H26N10O13P2S2/c21-19-26-14-8(16(34)28-19)25-5(1-23-14)12(46)13(47)6(31)2-40-44(36,37)43-45(38,39)41-3-7-10(32)11(33)18(42-7)30-4-24-9-15(30)27-20(22)29-17(9)35/h1,4-7,10-11,18,25,31-33,46-47H,2-3H2,(H,36,37)(H,38,39)(H3,21,26,28,34)(H3,22,27,29,35)/b13-12-/t5-,6-,7-,10-,11-,18-/m1/s1
InChIKey 
IRGDLSAXQOKWLX-XHEYTWMPSA-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
PF00384' 'PF01568

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_0600.

PDB 6

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)