Structure of PDB 2e3p Chain B Binding Site BS01

Receptor Information

>2e3p Chain B (length=231) Species: 9606 (Homo sapiens)

HRFVQKVEEMVQNHMTYSLQDVGGDANWQLVVEEGEMKVYRREVEENGIV
LDPLKATHAVKGVTGHEVCNYFWNVDVRNDWETTIENFHVVETLADNAII
IYQTHKRVWPASQRDVLYLSVIRKIPALTENDPETWIVCNFSVDHDSAPL
NNRCVRAKINVAMICQTLVSPPQEISRDNILCKITYVANVNPGGWAPASV
LRAVAKREYPKFLKRFTSYVQEKTAGKPILF

Ligand information

• Ligand ID: 16C
• InChI: InChI=1S/C34H67NO3/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-33(37)32(31-36)35-34(38)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h27,29,32-33,36-37H,3-26,28,30-31H2,1-2H3,(H,35,38)/b29-27+/t32-,33+/m0/s1
• InChIKey: YDNKGFDKKRUKPY-TURZORIXSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCCC(=O)NC(CO)C(C=CCCCCCCCCCCCCC)O
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@@H](\C=C\CCCCCCCCCCCCC)O
  ACDLabs 10.04: O=C(NC(CO)C(O)/C=C/CCCCCCCCCCCCC)CCCCCCCCCCCCCCC
  CACTVS 3.341: CCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)\C=C\CCCCCCCCCCCCC
  CACTVS 3.341: CCCCCCCCCCCCCCCC(=O)N[CH](CO)[CH](O)C=CCCCCCCCCCCCCC
• Formula: C34 H67 N O3
• Name: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE;
  C16-CERAMIDE;
  N-PALMITOYL-D-ERYTHRO-SPHINGOSINE;
  (2S,3R,4E)-2-PALMITOYLAMINOOCTADEC-4-ENE-1,3-DIOL;
  (2S,3R,4E)-2-PALMITOYLAMINO-1,3-OCTADEC-4-ENEDIOL
• ChEMBL: CHEMBL35292
• ZINC: ZINC000008860497
• PDB chain: 2e3p Chain B Residue 700

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2e3p Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): E446 H469 V472 A475 R478 N504 Y553 L568 Y576 F579
• Binding residue (residue number reindexed from 1): E82 H105 V108 A111 R114 N140 Y186 L201 Y209 F212
• Annotation score: 5

Gene Ontology

Molecular Function

• GO:0008289 lipid binding

External links

• PDB: RCSB:2e3p, PDBe:2e3p, PDBj:2e3p
• PDBsum: 2e3p
• PubMed: 18184806
• UniProt: Q9Y5P4|CERT_HUMAN Ceramide transfer protein (Gene Name=CERT1)