Structure of PDB 2r0n Chain A Binding Site BS02

Receptor Information
>2r0n 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 IDTGC
InChIInChI=1S/C25H40N7O19P3S2/c1-25(2,20(38)23(39)28-4-3-14(33)27-5-6-56-16(36)9-55-8-15(34)35)10-48-54(45,46)51-53(43,44)47-7-13-19(50-52(40,41)42)18(37)24(49-13)32-12-31-17-21(26)29-11-30-22(17)32/h11-13,18-20,24,37-38H,3-10H2,1-2H3,(H,27,33)(H,28,39)(H,34,35)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t13-,18-,19-,20+,24-/m1/s1
InChIKeyGKSSRSUPHZUOQO-ITIYDSSPSA-N
SMILES
SoftwareSMILES
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)CSCC(=O)O)O
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)CSCC(=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)CSCC(O)=O
ACDLabs 10.04O=C(O)CSCC(=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
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)CSCC(O)=O
FormulaC25 H40 N7 O19 P3 S2
Name3-thiaglutaryl-CoA;
(3R,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14,19-trioxo-2,4,6-trioxa-18,21-dithia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide
ChEMBL
DrugBank
ZINCZINC000197367232
PDB chain2r0n Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2r0n The effect of a Glu370Asp mutation in glutaryl-CoA dehydrogenase on proton transfer to the dienolate intermediate.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R94 S95 V99 P144 G240 F243 L246 N247 P320 Y369 E370 I379
Binding residue
(residue number reindexed from 1)		R92 S93 V97 P142 G238 F241 L244 N245 P318 Y367 E368 I377
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:2r0n, PDBe:2r0n, PDBj:2r0n
PDBsum2r0n
PubMed18020372
UniProtQ92947|GCDH_HUMAN Glutaryl-CoA dehydrogenase, mitochondrial (Gene Name=GCDH)

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