Structure of PDB 1udy Chain A Binding Site BS02

Receptor Information

>1udy Chain A (length=385) Species: 9823 (Sus scrofa)

GFSFELTEQQKEFQATARKFAREEIIPVAAEYDRTGEYPVPLLKRAWELG
LMNTHIPESFGGLGLGIIDSCLITEELAYGCTGVQTAIEANTLGQVPLII
GGNYQQQKKYLGRMTEEPLMCAYCVTEPGAGSDVAGIKTKAEKKGDEYII
NGQKMWITNGGKANWYFLLARSDPDPKAPASKAFTGFIVEADTPGVQIGR
KEINMGQRCSDTRGIVFEDVRVPKENVLTGEGAGFKIAMGTFDKTRPPVA
AGAVGLAQRALDEATKYALERKTFGKLLAEHQGISFLLADMAMKVELARL
SYQRAAWEIDSGRRNTYYASIAKAYAADIANQLATDAVQVFGGNGFNTEY
PVEKLMRDAKIYQIYEGTAQIQRIIIAREHIGRYK

Ligand information

• Ligand ID: CS8
• InChI: InChI=1S/C28H48N7O17P3S2/c1-4-5-6-10-56-13-19(37)57-11-9-30-18(36)7-8-31-26(40)23(39)28(2,3)14-49-55(46,47)52-54(44,45)48-12-17-22(51-53(41,42)43)21(38)27(50-17)35-16-34-20-24(29)32-15-33-25(20)35/h15-17,21-23,27,38-39H,4-14H2,1-3H3,(H,30,36)(H,31,40)(H,44,45)(H,46,47)(H2,29,32,33)(H2,41,42,43)/t17-,21-,22-,23+,27-/m1/s1
• InChIKey: JMFXDZKFFYUOAN-SVHODSNWSA-N
• SMILES:
  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)CSCCCCC
  OpenEye OEToolkits 1.5.0: CCCCCSCC(=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
  OpenEye OEToolkits 1.5.0: CCCCCSCC(=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: CCCCCSCC(=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
  CACTVS 3.341: CCCCCSCC(=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
• Formula: C28 H48 N7 O17 P3 S2
• Name: 3-THIAOCTANOYL-COENZYME A
• DrugBank: DB03415
• ZINC: ZINC000096068405
• PDB chain: 1udy Chain A Residue 400

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1udy Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): L103 Y133 S142 S191 F245 M249 F252 V259 R324 Y375 E376 G377 I381 I385
• Binding residue (residue number reindexed from 1): L93 Y123 S132 S181 F235 M239 F242 V249 R314 Y365 E366 G367 I371 I375
• Annotation score: 3

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:1udy, PDBe:1udy, PDBj:1udy
• PDBsum: 1udy
• PubMed: 12966080
• UniProt: P41367|ACADM_PIG Medium-chain specific acyl-CoA dehydrogenase, mitochondrial (Gene Name=ACADM)