Structure of PDB 4izd Chain B Binding Site BS01

Receptor Information
>4izd Chain B (length=259) Species: 246200 (Ruegeria pomeroyi DSS-3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TQDVTSGYSNLDLDLRDNGVCVVTLNRPDKRNALDVATIEELVTFFSTAH
RKGVRAVVLTGAGDHFCAGLDLVEHWKADRSADDFMHVCLRWHEAFNKME
YGGVPIIAALRGAVVGGGLALASAAHLRVMDQSTYFALPEGQRGIFTGGG
ATIRVSDMIGKYRMIDMILTGRVYQGQEAADLGLAQYITEGSSFDKAMEL
ADKIASNLPLTNFAICSAISHMQNMSGLDAAYAEAFVGGIVNTQPAARER
LEAFANKTA
Ligand information
Ligand ID1HE
InChIInChI=1S/C25H42N7O17P3S2/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/h12-14,18-20,24,35-36H,4-11H2,1-3H3,(H,27,33)(H,28,37)(H,41,42)(H,43,44)(H2,26,29,30)(H2,38,39,40)/t14-,18-,19-,20+,24-/m1/s1
InChIKeySIEFLYWJLBNLAM-CITAKDKDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(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)CCSC)O
OpenEye OEToolkits 1.7.6CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)CCSC)O
CACTVS 3.370CSCCC(=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
CACTVS 3.370CSCCC(=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
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)CCSC
FormulaC25 H42 N7 O17 P3 S2
Name3-methylmercaptopropionate-CoA (MMPA-CoA)
ChEMBL
DrugBank
ZINCZINC000198971969
PDB chain4izd Chain B 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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PDB4izd 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)		D30 K31 R32 A34 A69 L71 D72 L73 W93 G117 G118 E141 R144 G149
Binding residue
(residue number reindexed from 1)		D29 K30 R31 A33 A68 L70 D71 L72 W92 G116 G117 E140 R143 G148
Annotation score3
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) L70 H75 C89 H93 G117 A120 E140 G148 Y232
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:4izd, PDBe:4izd, PDBj:4izd
PDBsum4izd
PubMed23704947
UniProtQ5LLW6|DMDD_RUEPO Methylthioacryloyl-CoA hydratase (Gene Name=dmdD)

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