Structure of PDB 3mde Chain B Binding Site BS02

Receptor Information

>3mde Chain B (length=385) Species: 9823 (Sus scrofa)

GFSFELTEQQKEFQATARKFAREEIIPVAAEYDRTGEYPVPLLKRAWELG
LMNTHIPESFGGLGLGIIDSCLITEELAYGCTGVQTAIEANTLGQVPLII
GGNYQQQKKYLGRMTEEPLMCAYCVTEPGAGSDVAGIKTKAEKKGDEYII
NGQKMWITNGGKANWYFLLARSDPDPKAPASKAFTGFIVEADTPGVQIGR
KEINMGQRCSDTRGIVFEDVRVPKENVLTGEGAGFKIAMGTFDKTRPPVA
AGAVGLAQRALDEATKYALERKTFGKLLAEHQGISFLLADMAMKVELARL
SYQRAAWEIDSGRRNTYYASIAKAYAADIANQLATDAVQVFGGNGFNTEY
PVEKLMRDAKIYQIYEGTAQIQRIIIAREHIGRYK

Ligand information

• Ligand ID: CO8
• InChI: InChI=1S/C29H50N7O17P3S/c1-4-5-6-7-8-9-20(38)57-13-12-31-19(37)10-11-32-27(41)24(40)29(2,3)15-50-56(47,48)53-55(45,46)49-14-18-23(52-54(42,43)44)22(39)28(51-18)36-17-35-21-25(30)33-16-34-26(21)36/h16-18,22-24,28,39-40H,4-15H2,1-3H3,(H,31,37)(H,32,41)(H,45,46)(H,47,48)(H2,30,33,34)(H2,42,43,44)/t18-,22-,23-,24+,28-/m1/s1
• InChIKey: KQMZYOXOBSXMII-CECATXLMSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  ACDLabs 10.04: O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)CCCCCCC
  OpenEye OEToolkits 1.5.0: CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  CACTVS 3.341: CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  CACTVS 3.341: CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
• Formula: C29 H50 N7 O17 P3 S
• Name: OCTANOYL-COENZYME A
• DrugBank: DB02910
• ZINC: ZINC000096014975
• PDB chain: 3mde Chain B Residue 400

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3mde Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): T96 E99 L103 G141 S142 V144 S191 F245 M249 F252 Y375 E376 G377
• Binding residue (residue number reindexed from 1): T86 E89 L93 G131 S132 V134 S181 F235 M239 F242 Y365 E366 G367
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): V135 T136 T255 E376 R388
• Catalytic site (residue number reindexed from 1): V125 T126 T245 E366 R378
• Enzyme Commision number: 1.3.8.7: medium-chain acyl-CoA dehydrogenase.

Gene Ontology

Molecular Function

• GO:0003995 acyl-CoA dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
• GO:0042802 identical protein binding
• GO:0050660 flavin adenine dinucleotide binding
• GO:0070991 medium-chain fatty acyl-CoA dehydrogenase activity

Biological Process

• GO:0001889 liver development
• GO:0005978 glycogen biosynthetic process
• GO:0006082 organic acid metabolic process
• GO:0006111 regulation of gluconeogenesis
• GO:0006631 fatty acid metabolic process
• GO:0006635 fatty acid beta-oxidation
• GO:0007507 heart development
• GO:0009409 response to cold
• GO:0009437 carnitine metabolic process
• GO:0009791 post-embryonic development
• GO:0019254 carnitine metabolic process, CoA-linked
• GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase
• GO:0042594 response to starvation
• GO:0045329 carnitine biosynthetic process
• GO:0051791 medium-chain fatty acid metabolic process
• GO:0051793 medium-chain fatty acid catabolic process
• GO:0055007 cardiac muscle cell differentiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0030424 axon
• GO:0031966 mitochondrial membrane

External links

• PDB: RCSB:3mde, PDBe:3mde, PDBj:3mde
• PDBsum: 3mde
• PubMed: 8356049
• UniProt: P41367|ACADM_PIG Medium-chain specific acyl-CoA dehydrogenase, mitochondrial (Gene Name=ACADM)