Ligand profile

3CD

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

Bound to: VK055_4126 — erythrose-4-phosphate dehydrogenase

Via homolog PDB 2xf8 UniProt P0A9B6 Formula C₂₂H₂₈ClN₆O₁₄P₂⁺
Mol. weight 697.90 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3CD
PDB
2xf8
UniProt (similar protein)
P0A9B6
Target protein
VK055_4126

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 697.90 Da
LogP (Crippen) -1.69
H-bond donors 7
H-bond acceptors 17
TPSA 292.24 Ų
Rotatable bonds 12
Aromatic rings 3 / 5
Heavy atoms 45
Fraction sp³ C 0.50
Formula C₂₂H₂₈ClN₆O₁₄P₂⁺

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 292.2
  • −1 ≤ LogP ≤ 5 -1.69
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 697.9
  • LogP ≤ 5 -1.69
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 292.2
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)n4cnc5c4ncnc5N)O)O)O)O)C(=O)CCl
InChI 
InChI=1S/C22H27ClN6O14P2/c23-4-11(30)10-2-1-3-28(5-10)21-17(33)15(31)12(41-21)6-39-44(35,36)43-45(37,38)40-7-13-16(32)18(34)22(42-13)29-9-27-14-19(24)25-8-26-20(14)29/h1-3,5,8-9,12-13,15-18,21-22,31-34H,4,6-7H2,(H3-,24,25,26,35,36,37,38)/p+1/t12-,13-,15-,16-,17-,18-,21-,22-/m1/s1
InChIKey 
XIQCGHNADRRDKB-RBEMOOQDSA-O

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
PF00044

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_4126.

PDB 7

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

Ligand PDB entry

ChEMBL 2

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)