Structure of PDB 1egd Chain D Binding Site BS02

Receptor Information

>1egd Chain D (length=387) Species: 9606 (Homo sapiens)

LGFSFEFTEQQKEFQATARKFAREEIIPVAAEYDKTGEYPVPLIRRAWEL
GLMNTHIPENCGGLGLGTFDACLISEELAYGCTGVQTAIEGNSLGQMPII
IAGNDQQKKKYLGRMTEEPLMCAYCVTEPGAGSDVAGIKTKAEKKGDEYI
INGQKMWITNGGKANWYFLLARSDPDPKAPANKAFTGFIVEADTPGIQIG
RKELNMGQRCSDTRGIVFEDVKVPKENVLIGDGAGFKVAMGAFDKERPVV
AAGAVGLAQRALDEATKYALERKTFGKLLVEHQAISFMLAEMAMKVELAR
MSYQRAAWEVDSGRRNTYYASIAKAFAGDIANQLATDAVQILGGNGFNTE
YPVEKLMRDAKIYQIYGGTSQIQRLIVAREHIDKYKN

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 1egd Chain D Residue 399

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1egd Crystal structures of the wild type and the Glu376Gly/Thr255Glu mutant of human medium-chain acyl-CoA dehydrogenase: influence of the location of the catalytic base on substrate specificity.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): Y133 V135 T136 G141 S142 W166 T168 Y375 T378 Q380
• Binding residue (residue number reindexed from 1): Y124 V126 T127 G132 S133 W157 T159 Y366 T369 Q371
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): V135 T136 E255 G376 R388
• Catalytic site (residue number reindexed from 1): V126 T127 E246 G367 R379
• 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:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0030424 axon
• GO:0031966 mitochondrial membrane

External links

• PDB: RCSB:1egd, PDBe:1egd, PDBj:1egd
• PDBsum: 1egd
• PubMed: 8823176
• UniProt: P11310|ACADM_HUMAN Medium-chain specific acyl-CoA dehydrogenase, mitochondrial (Gene Name=ACADM)