Structure of PDB 1sir Chain A Binding Site BS02

Receptor Information
>1sir Chain A (length=390) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFDWQDPLVLEEQLTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREI
ISEMGELGVLGPTIKGYGCAGVSSVAYGLLARELERVDSGYRSAMSVQSS
LVMHPIYAYGSEEQRQKYLPQLAKGELLGCFGLTEPNSGSDPSSMETRAH
YNSSNKSYTLNGTKTWITNSPMADLFVVWARCEDGCIRGFLLEKGMRGLS
APRIQGKFSLRASATGMIIMDGVEVPEENVLPGASSLGGPFGCLNNARYG
IAWGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKLADMLTEITLG
LHACLQLGRLKDQDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISD
EYHVIRHAMNLEAVNTYEGTHDIHALILGRAITGIQAFTA
Ligand information
Ligand IDNBC
InChIInChI=1S/C25H41N8O19P3S/c1-25(2,20(37)23(38)28-6-5-15(34)27-7-9-56-16(35)4-3-8-33(39)40)11-49-55(46,47)52-54(44,45)48-10-14-19(51-53(41,42)43)18(36)24(50-14)32-13-31-17-21(26)29-12-30-22(17)32/h12-14,18-20,24,36-37H,3-11H2,1-2H3,(H,27,34)(H,28,38)(H,44,45)(H,46,47)(H2,26,29,30)(H2,41,42,43)/t14-,18-,19-,20+,24-/m1/s1
InChIKeyPXNIOQHGCSEKCC-CITAKDKDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(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)[C@H](C(=O)NCCC(=O)NCCSC(=O)CCC[N+](=O)[O-])O
CACTVS 3.341CC(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)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)CCC[N+]([O-])=O
CACTVS 3.341CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)CCC[N+]([O-])=O
OpenEye OEToolkits 1.5.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)CCC[N+](=O)[O-])O
ACDLabs 10.04[O-][N+](=O)CCCC(=O)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
FormulaC25 H41 N8 O19 P3 S
NameS-4-NITROBUTYRYL-COA
ChEMBL
DrugBankDB03245
ZINCZINC000195757740
PDB chain1sir Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1sir Crystal Structures of Human Glutaryl-CoA Dehydrogenase with and without an Alternate Substrate: Structural Bases of Dehydrogenation and Decarboxylation Reactions
Resolution2.6 Å
Binding residue
(original residue number in PDB)		S95 S142 F243 G244 L246 N247 R250 P320 Y369 E370 R382
Binding residue
(residue number reindexed from 1)		S93 S140 F241 G242 L244 N245 R248 P318 Y367 E368 R380
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) L135 T136 A249 E370 R382
Catalytic site (residue number reindexed from 1) L133 T134 A247 E368 R380
Enzyme Commision number 1.3.8.6: glutaryl-CoA dehydrogenase (ETF).
Gene Ontology
Molecular Function
GO:0000062 fatty-acyl-CoA binding
GO:0003995 acyl-CoA dehydrogenase activity
GO:0004361 glutaryl-CoA dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0006568 tryptophan metabolic process
GO:0006637 acyl-CoA metabolic process
GO:0019395 fatty acid oxidation
GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase
GO:0046949 fatty-acyl-CoA biosynthetic process
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1sir, PDBe:1sir, PDBj:1sir
PDBsum1sir
PubMed15274622
UniProtQ92947|GCDH_HUMAN Glutaryl-CoA dehydrogenase, mitochondrial (Gene Name=GCDH)

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