Structure of PDB 7ymr Chain B Binding Site BS01

Receptor Information

>7ymr Chain B (length=301) Species: 1424779 (Thermocrispum sp. RD004668)

DNPWLDARVLNMAHAGGENEAPANTLYAFKRAVKLGANMLELDVQSTKDD
QLVVIHNATVDQTTDGTGKVRDLTFEQVHELDAAYNFIPGRHAVPGEPPE
SYPLRGVRTGEKKPPPGYQPSDFAIPKLADVLEAFPRTPINIEIKGTSDA
DIPSFLHNAKLLARLLKKTGRTDFIVTSLNDLAVAKFHLLAPDIPIAPGM
AGLAAYFLLGVKPMHGTVALQIPVRYQGLEIATPEFIRRAHADGYAVHVW
FSGTAPDDEATYNRIIDSCADGLMPAYPALLERILDERGIERPGRPGVDP
C

Ligand information

• Ligand ID: KIP
• InChI: InChI=1S/C24H50NO7P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-24(27)30-21-23(26)22-32-33(28,29)31-20-19-25(2,3)4/h23,26H,5-22H2,1-4H3/p+1/t23-/m1/s1
• InChIKey: ASWBNKHCZGQVJV-HSZRJFAPSA-O
• SMILES:
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCC[N+](C)(C)C)O
  CACTVS 3.385: CCCCCCCCCCCCCCCC(=O)OC[CH](O)CO[P](O)(=O)OCC[N+](C)(C)C
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCC[N+](C)(C)C)O
  CACTVS 3.385: CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P](O)(=O)OCC[N+](C)(C)C
• Formula: C24 H51 N O7 P
• Name: [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{5}-azanyl)ethoxy]phosphoryl]oxy-propyl] hexadecanoate
• ZINC: ZINC000008214423
• PDB chain: 7ymr Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ymr Structural basis for the substrate specificity switching of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. RD004668.
• Resolution: 2.69 Å
• Binding residue (original residue number in PDB): H46 E50 H88 E175 K177 L211 L235 Q253 Y258 W282 S284
• Binding residue (residue number reindexed from 1): H14 E18 H56 E143 K145 L179 L203 Q221 Y226 W250 S252
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0008081 phosphoric diester hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006629 lipid metabolic process

External links

• PDB: RCSB:7ymr, PDBe:7ymr, PDBj:7ymr
• PDBsum: 7ymr
• PubMed: 36307380
• UniProt: A0A0U4VTN7