Structure of PDB 6y79 Chain P Binding Site BS01

Receptor Information

>6y79 Chain P (length=123) Species: 4952 (Yarrowia lipolytica)

AIIATAFAETVKFSGSKQELQKRTLALYRQFLRGAPTFADLYEVQFSIPT
IRTKIRQEFERHRFVDDLSIQNVLYAKGHMEYQECINAWKQQAQFLKYFP
EEDDIQGRHQPSNFVDKFLKNRA

Ligand information

• Ligand ID: ZMP
• InChI: InChI=1S/C25H49N2O8PS/c1-4-5-6-7-8-9-10-11-12-13-14-15-22(29)37-19-18-26-21(28)16-17-27-24(31)23(30)25(2,3)20-35-36(32,33)34/h23,30H,4-20H2,1-3H3,(H,26,28)(H,27,31)(H2,32,33,34)/t23-/m1/s1
• InChIKey: HDTINWYIVVMRIN-HSZRJFAPSA-N
• SMILES:
  CACTVS 3.385: CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](O)C(C)(C)CO[P](O)(O)=O
  OpenEye OEToolkits 2.0.5: CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)O)O
  ACDLabs 12.01: OP(=O)(OCC(C(C(NCCC(=O)NCCSC(=O)CCCCCCCCCCCCC)=O)O)(C)C)O
  CACTVS 3.385: CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(O)=O
  OpenEye OEToolkits 2.0.5: CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(C)COP(=O)(O)O)O
• Formula: C25 H49 N2 O8 P S
• Name: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
• ZINC: ZINC000145431082
• PDB chain: 6y79 Chain O Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6y79 Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I.
• Resolution: 2.96 Å
• Binding residue (original residue number in PDB): T25 F32 E59 F60 H63 R64 Q72 L75 F96 F100
• Binding residue (residue number reindexed from 1): T24 F31 E58 F59 H62 R63 Q71 L74 F95 F99
• Annotation score: 1

Gene Ontology

Biological Process

• GO:0006979 response to oxidative stress

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0045271 respiratory chain complex I

External links

• PDB: RCSB:6y79, PDBe:6y79, PDBj:6y79
• PDBsum: 6y79
• PubMed: 33243981
• UniProt: Q6CI60