Structure of PDB 1opb Chain D Binding Site BS01

Receptor Information

>1opb Chain D (length=133) Species: 10117 (Rattus rattus)

TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFK
TKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGE
KENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK

Ligand information

• Ligand ID: RET
• InChI: InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6+,12-11+,16-8+,17-13+
• InChIKey: NCYCYZXNIZJOKI-OVSJKPMPSA-N
• SMILES:
  CACTVS 3.370: CC(=C\C=O)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C
  ACDLabs 12.01: O=C\C=C(\C=C\C=C(\C=C\C1=C(C)CCCC1(C)C)C)C
  OpenEye OEToolkits 1.7.0: CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C=O)/C)/C
  OpenEye OEToolkits 1.7.0: CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CC=O)C)C
  CACTVS 3.370: CC(=CC=O)C=CC=C(C)C=CC1=C(C)CCCC1(C)C
• Formula: C20 H28 O
• Name: RETINAL
• ChEMBL: CHEMBL81379
• ZINC: ZINC000004228262
• PDB chain: 1opb Chain D Residue 134

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1opb Crystal structures of holo and apo-cellular retinol-binding protein II.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): K40 L77 W106 Q108
• Binding residue (residue number reindexed from 1): K40 L77 W106 Q108
• Annotation score: 4
• Binding affinity: MOAD: Kd=50nM

Gene Ontology

Molecular Function

• GO:0005504 fatty acid binding
• GO:0008289 lipid binding
• GO:0016918 retinal binding
• GO:0019841 retinol binding

Biological Process

• GO:0015908 fatty acid transport
• GO:0042572 retinol metabolic process

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:1opb, PDBe:1opb, PDBj:1opb
• PDBsum: 1opb
• PubMed: 8487303
• UniProt: P06768|RET2_RAT Retinol-binding protein 2 (Gene Name=Rbp2)