Structure of PDB 1u8v Chain D Binding Site BS03

Receptor Information
>1u8v Chain D (length=490) Species: 33953 (Clostridium aminobutyricum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLMTAEQYIESLRKLNTRVYMFGEKIENWVDHPMIRPSINCVRMTYELAQ
DPQYADLMTTKSNLIGKTINRFANLHQSTDDLRKKVKMQRLLGQKTASCF
QRCVGMDAFNAVFSTTYEIDQKYGTNYHKNFTEYLKYIQENDLIVDGAMT
DPKGDRGLAPSAQKDPDLFLRIVEKREDGIVVRGAKAHQTGSINSHEHII
MPTIAMTEADKDYAVSFACPSDADGLFMIYGRQSCDTRKMEEGADIDLGN
KQFGGQEALVVFDNVFIPNDRIFLCQEYDFAGMMVERFAGYHRQSYGGCK
VGVGDVVIGAAALAADYNGAQKASHVKDKLIEMTHLNETLYCCGIACSAE
GYPTAAGNYQIDLLLANVCKQNITRFPYEIVRLAEDIAGGLMVTMPSEAD
FKSETVVGRDGETIGDFCNKFFAAAPTCTTEERMRVLRFLENICLGASAV
GYRTESMHGAGSPQAQRIMIARQGNINAKKELAKAIAGIK
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 chain1u8v Chain D Residue 492 [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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PDB1u8v Crystal structure of 4-hydroxybutyryl-CoA dehydratase: radical catalysis involving a [4Fe-4S] cluster and flavin.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		T150 K153 R156 H188 Q189 T190 E455 H458
Binding residue
(residue number reindexed from 1)		T150 K153 R156 H188 Q189 T190 E455 H458
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C99 C103 T190 E257 H292 Y296 C299 E455
Catalytic site (residue number reindexed from 1) C99 C103 T190 E257 H292 Y296 C299 E455
Enzyme Commision number 4.2.1.120: 4-hydroxybutanoyl-CoA dehydratase.
5.3.3.3: vinylacetyl-CoA Delta-isomerase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0016829 lyase activity
GO:0016853 isomerase activity
GO:0043721 4-hydroxybutanoyl-CoA dehydratase activity
GO:0046872 metal ion binding
GO:0050393 vinylacetyl-CoA delta-isomerase activity
GO:0051539 4 iron, 4 sulfur cluster binding

View graph for
Molecular Function
External links
PDB RCSB:1u8v, PDBe:1u8v, PDBj:1u8v
PDBsum1u8v
PubMed15496473
UniProtP55792|HDVD_CLOAM 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase (Gene Name=abfD)

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