Ligand profile

EE1

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

Bound to: VK055_1318 — isocitrate dehydrogenase, NADP-dependent

Via homolog PDB 6c0e UniProt Q5ZXB6 Formula C₂₆H₃₄N₇O₂₂P₃
Mol. weight 889.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EE1
PDB
6c0e
UniProt (similar protein)
Q5ZXB6
Target protein
VK055_1318

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 889.51 Da
LogP (Crippen) -3.60
H-bond donors 11
H-bond acceptors 22
TPSA 455.82 Ų
Rotatable bonds 18
Aromatic rings 2 / 5
Heavy atoms 58
Fraction sp³ C 0.50
Formula C₂₆H₃₄N₇O₂₂P₃

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 455.8
  • −1 ≤ LogP ≤ 5 -3.60
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 889.5
  • LogP ≤ 5 -3.60
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 22
Veber's rules Fail
  • Rotatable bonds ≤ 10 18
  • TPSA ≤ 140 Ų 455.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=C[C@H](C(=C5)C(=O)N)[C@H](CC(=O)O)C(=O)C(=O)O)O)O)O)OP(=O)(O)O)N
InChI 
InChI=1S/C26H34N7O22P3/c27-21-15-23(30-7-29-21)33(8-31-15)25-20(54-56(43,44)45)18(38)13(53-25)6-51-58(48,49)55-57(46,47)50-5-12-17(37)19(39)24(52-12)32-2-1-9(11(4-32)22(28)40)10(3-14(34)35)16(36)26(41)42/h1-2,4,7-10,12-13,17-20,24-25,37-39H,3,5-6H2,(H2,28,40)(H,34,35)(H,41,42)(H,46,47)(H,48,49)(H2,27,29,30)(H2,43,44,45)/t9-,10-,12+,13+,17+,18+,19+,20+,24+,25+/m0/s1
InChIKey 
WSGZIHXYYXDDDT-PJNAXEGASA-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
PF00180

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_1318.

PDB 10

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)