Ligand profile

NBP

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

Bound to: VK055_5026 — 6-phosphogluconate dehydrogenase

Via homolog PDB 1pgn UniProt P00349 Formula C₂₁H₂₇BrN₇O₁₇P₃
Mol. weight 822.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NBP
PDB
1pgn
UniProt (similar protein)
P00349
Target protein
VK055_5026

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 822.31 Da
LogP (Crippen) -2.77
H-bond donors 8
H-bond acceptors 19
TPSA 367.62 Ų
Rotatable bonds 13
Aromatic rings 3 / 5
Heavy atoms 49
Fraction sp³ C 0.48
Formula C₂₁H₂₇BrN₇O₁₇P₃

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 367.6
  • −1 ≤ LogP ≤ 5 -2.77
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 822.3
  • LogP ≤ 5 -2.77
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 367.6
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)n4c5c(c(ncn5)N)nc4Br)OP(=O)(O)O)O)O)O)C(=O)N
InChI 
InChI=1S/C21H27BrN7O17P3/c22-21-27-11-16(23)25-7-26-18(11)29(21)20-15(45-47(34,35)36)13(31)10(44-20)6-42-49(39,40)46-48(37,38)41-5-9-12(30)14(32)19(43-9)28-3-1-2-8(4-28)17(24)33/h1-4,7,9-10,12-15,19-20,30-32H,5-6H2,(H7-,23,24,25,26,33,34,35,36,37,38,39,40)/t9-,10-,12-,13-,14-,15-,19-,20-/m1/s1
InChIKey 
MDKMTCCUJSRQGW-NAJQWHGHSA-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
PF03446

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_5026.

PDB 6

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

Ligand PDB entry

ChEMBL 4

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)