Structure of PDB 4izc Chain A Binding Site BS01

Receptor Information
>4izc Chain A (length=251) Species: 246200 (Ruegeria pomeroyi DSS-3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QDVTSGYSNLDLDLRDNGVCVVTLNRPDKRNALDVATIEELVTFFSTAHR
KGVRAVVLTGAGDHFCAGLDLVEHWKADRSADDFMHVCLRWHEAFNKMEY
GGVPIIAALRGAVVGGGLALASAAHLRVMDQSTYFALPEGQRGIFTGGGA
TIRVSDMIGKYRMIDMILTGRVYQGQEAADLGLAQYITEGSSFDKAMELA
DKIASNLPLTNFAICSAISHMQNMSGLDAAYAEAFVGGIVNTQPAARERL
E
Ligand information
Ligand ID1GZ
InChIInChI=1S/C25H40N7O17P3S2/c1-25(2,20(36)23(37)28-6-4-15(33)27-7-9-54-16(34)5-8-53-3)11-46-52(43,44)49-51(41,42)45-10-14-19(48-50(38,39)40)18(35)24(47-14)32-13-31-17-21(26)29-12-30-22(17)32/h5,8,12-14,18-20,24,35-36H,4,6-7,9-11H2,1-3H3,(H,27,33)(H,28,37)(H,41,42)(H,43,44)(H2,26,29,30)(H2,38,39,40)/b8-5+/t14-,18-,19-,20+,24-/m1/s1
InChIKeyZGBNNHAIMKRDOC-CABWFRLRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CSC=CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.9.2CC(C)(COP(=O)(O)OP(=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)/C=C/SC)O
ACDLabs 12.01O=C(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)\C=C\SC
OpenEye OEToolkits 1.9.2CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)C=CSC)O
CACTVS 3.385CS/C=C/C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(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
FormulaC25 H40 N7 O17 P3 S2
Namemethylthioacryloyl-CoA
ChEMBL
DrugBank
ZINCZINC000198971630
PDB chain4izc Chain A Residue 301 [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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PDB4izc Crystal Structure of DmdD, a Crotonase Superfamily Enzyme That Catalyzes the Hydration and Hydrolysis of Methylthioacryloyl-CoA.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		K31 R32 A34 A69 G70 L71 D72 L73 V116 G117 G118 T148 G149
Binding residue
(residue number reindexed from 1)		K29 R30 A32 A67 G68 L69 D70 L71 V114 G115 G116 T146 G147
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) L71 H76 C90 H94 G118 A121 E141 G149 Y233
Catalytic site (residue number reindexed from 1) L69 H74 C88 H92 G116 A119 E139 G147 Y231
Enzyme Commision number 4.2.1.155: methylthioacryloyl-CoA hydratase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004300 enoyl-CoA hydratase activity
GO:0016829 lyase activity
GO:0016836 hydro-lyase activity
Biological Process
GO:0006635 fatty acid beta-oxidation
GO:0034214 protein hexamerization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4izc, PDBe:4izc, PDBj:4izc
PDBsum4izc
PubMed23704947
UniProtQ5LLW6|DMDD_RUEPO Methylthioacryloyl-CoA hydratase (Gene Name=dmdD)

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