Structure of PDB 4zdc Chain B Binding Site BS01

Receptor Information
>4zdc Chain B (length=262) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIRQNEKISYRIEGPFFIIHLINPDNLNALEGEDYIYLGELLELADRNRD
VYFTIIQSSGRFFSSGADFKGIAKAQKYPSETSKWVSNFVARNVYVTDAF
IKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITE
GGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEA
FNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKY
WVDGEPLKRFRQ
Ligand information
Ligand IDCO8
InChIInChI=1S/C29H50N7O17P3S/c1-4-5-6-7-8-9-20(38)57-13-12-31-19(37)10-11-32-27(41)24(40)29(2,3)15-50-56(47,48)53-55(45,46)49-14-18-23(52-54(42,43)44)22(39)28(51-18)36-17-35-21-25(30)33-16-34-26(21)36/h16-18,22-24,28,39-40H,4-15H2,1-3H3,(H,31,37)(H,32,41)(H,45,46)(H,47,48)(H2,30,33,34)(H2,42,43,44)/t18-,22-,23-,24+,28-/m1/s1
InChIKeyKQMZYOXOBSXMII-CECATXLMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
ACDLabs 10.04O=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)CCCCCCC
OpenEye OEToolkits 1.5.0CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(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)O
CACTVS 3.341CCCCCCCC(=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
CACTVS 3.341CCCCCCCC(=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
FormulaC29 H50 N7 O17 P3 S
NameOCTANOYL-COENZYME A
ChEMBL
DrugBankDB02910
ZINCZINC000096014975
PDB chain4zdc Chain B Residue 304 [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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PDB4zdc Structures of yeast peroxisomal Delta (3), Delta (2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole.
Resolution2.13 Å
Binding residue
(original residue number in PDB)		N29 L30 A32 F65 S68 D71 F72 K73
Binding residue
(residue number reindexed from 1)		N26 L27 A29 F62 S65 D68 F69 K70
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) A70 N101 L126 A129 F150 E158
Catalytic site (residue number reindexed from 1) A67 N93 L118 A121 F142 E150
Enzyme Commision number 5.3.3.8: Delta(3)-Delta(2)-enoyl-CoA isomerase.
Gene Ontology
Molecular Function
GO:0004165 delta(3)-delta(2)-enoyl-CoA isomerase activity
GO:0016853 isomerase activity
Biological Process
GO:0006631 fatty acid metabolic process
GO:0006635 fatty acid beta-oxidation
Cellular Component
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4zdc, PDBe:4zdc, PDBj:4zdc
PDBsum4zdc
PubMed26527136
UniProtQ05871|ECI1_YEAST 3,2-trans-enoyl-CoA isomerase (Gene Name=ECI1)

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