Structure of PDB 4p13 Chain A Binding Site BS01

Receptor Information
>4p13 Chain A (length=387) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LGFSFEFTEQQKEFQATARKFAREEIIPVAAEYDKTGEYPVPLIRRAWEL
GLMNTHIPENCGGLGLGTFDACLISEELAYGCTGVQTAIEGNSLGQMPII
IAGNDQQKKKYLGRMTEEPLMCAYCVTEPGAGSDVAGIKTKAEKKGDEYI
INGQKMWITNGGKANWYFLLARSDPDPKAPANKAFTGFIVEADTPGIQIG
RKELNMGQRCSDTRGIVFEDVKVPKENVLIGDGAGFKVAMGAFDKTRPVV
AAGAVGLAQRALDEATKYALERKTFGKLLVEHQAISFMLAEMAMEVELAR
MSYQRAAWEVDSGRRNTYYASIAKAFAGDIANQLATDAVQILGGNGFNTE
YPVEKLMRDAKIYQIYEGTSQIQRLIVAREHIDKYKN
Ligand information
Ligand IDFAD
InChIInChI=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
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=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 1.5.0Cc1cc2c(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 1.5.0Cc1cc2c(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 3.341Cc1cc2N=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 10.04O=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
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain4p13 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4p13 Medium chain acyl-CoA dehydrogenase, K304E mutant
Resolution1.73 Å
Binding residue
(original residue number in PDB)		Y133 V135 T136 G141 S142 W166 I167 T168 I371 Y375 T378 Q380
Binding residue
(residue number reindexed from 1)		Y124 V126 T127 G132 S133 W157 I158 T159 I362 Y366 T369 Q371
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) V135 T136 T255 E376 R388
Catalytic site (residue number reindexed from 1) V126 T127 T246 E367 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4p13, PDBe:4p13, PDBj:4p13
PDBsum4p13
PubMed
UniProtP11310|ACADM_HUMAN Medium-chain specific acyl-CoA dehydrogenase, mitochondrial (Gene Name=ACADM)

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