Structure of PDB 5d92 Chain A Binding Site BS03

Receptor Information

>5d92 Chain A (length=340) Species: 224325,288705

MRLAYVKNHEIYGEKLLGLTLRERIEKTLQRAGFDVRFFDELSLEEAEDY
LIILEPVLILERDLLLEGRKILVSDGFTVGYFFGGDFRTVFDGNLQSSIE
KYLSLNNLESYEIWAIKLSNDNLKTAEKLLLSSLIGSGSKYARGLFAAIF
LPIARLLADWGVSPDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVF
SDIIDGLMARLLFREGPWGAFLDSYLDRVGDSSVFTGIVIWFFLGGANPT
IAILALICLVLSSLVSYSKARAEGLGLTANVGIAERSERLVVVLVATGLV
GLGIPSWVLLVVLIVLAIASVVTIFQRVLTVREQAKAWTA

Ligand information

• Ligand ID: 58A
• InChI: InChI=1S/C48H85N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-43(52)61-37-40(64-44(53)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2)38-62-67(57,58)66-68(59,60)63-39-41-45(54)46(55)47(65-41)51-36-35-42(49)50-48(51)56/h17-20,35-36,40-41,45-47,54-55H,3-16,21-34,37-39H2,1-2H3,(H,57,58)(H,59,60)(H2,49,50,56)/b19-17+,20-18+/t40-,41-,45-,46-,47-/m1/s1
• InChIKey: WVVFFOKRFKIBHD-ZIPNUMAKSA-N
• SMILES:
  CACTVS 3.385: CCCCCCCCC=CCCCCCCCC(=O)OC[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N)OC(=O)CCCCCCCC=CCCCCCCCC
  ACDLabs 12.01: O=C1N(C=CC(=N1)N)C2OC(C(C2O)O)COP(=O)(O)OP(O)(OCC(COC(CCCCCCC\C=C\CCCCCCCC)=O)OC(CCCCCCCC=[C@H]CCCCCCCC)=O)=O
  OpenEye OEToolkits 1.9.2: CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)OC(=O)CCCCCCCC=CCCCCCCCC
  OpenEye OEToolkits 1.9.2: CCCCCCCCC=CCCCCCCCC(=O)OCC(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O)OC(=O)CCCCCCCC=CCCCCCCCC
  CACTVS 3.385: CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N)OC(=O)CCCCCCC\C=C\CCCCCCCC
• Formula: C48 H85 N3 O15 P2
• Name: 5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine;
  cytidinediphosphate-dioleoylglycerol;
  CDP-1,2-dioleoyl-sn-glycerol
• PDB chain: 5d92 Chain A Residue 311

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d92 Structural basis for phosphatidylinositol-phosphate biosynthesis.
• Resolution: 3.62 Å
• Binding residue (original residue number in PDB): D29 T32 T60 V63 F64 D66 I67 D69 G70 A73 E79 G83 A84 D87 S151 V155
• Binding residue (residue number reindexed from 1): D165 T168 T196 V199 F200 D202 I203 D205 G206 A209 E215 G219 A220 D223 S287 V291
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number:
  2.7.8.-

Gene Ontology

Molecular Function

• GO:0016780 phosphotransferase activity, for other substituted phosphate groups

Biological Process

• GO:0008654 phospholipid biosynthetic process

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:5d92, PDBe:5d92, PDBj:5d92
• PDBsum: 5d92
• PubMed: 26510127
• UniProt: A9WSF5;
  O27985