Structure of PDB 3o3n Chain C Binding Site BS02

Receptor Information
>3o3n Chain C (length=401) Species: 1496 (Clostridioides difficile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKEARVVINDLLAEQYANAFKAKEEGRPVGWSTSVFPQELAEVFDLNVLY
PENQAAGVAAKKGSLELCEIAESKGYSIDLCAYARTNFGLLENGGCEALD
MPAPDFLLCCNNICNQVIKWYENISRELDIPLIMIDTTFNNEDEVTQSRI
DYIKAQFEEAIKQLEIISGKKFDPKKFEEVMKISAENGRLWKYSMSLPAD
SSPSPMNGFDLFTYMAVIVCARGKKETTEAFKLLIEELEDNMKTGKSSFR
GEEKYRIMMEGIPCWPYIGYKMKTLAKFGVNMTGSVYPHAWALQYEVNDL
DGMAVAYSTMFNNVNLDRMTKYRVDSLVEGKCDGAFYHMNRSCKLMSLIQ
YEMQRRAAEETGLPYAGFDGDQADPRAFTNAQFETRIQGLVEVMEERKKL
N
Ligand information
Ligand IDIRC
InChIInChI=1S/C27H46N7O18P3S/c1-14(2)9-15(35)26(40)56-8-7-29-17(36)5-6-30-24(39)21(38)27(3,4)11-49-55(46,47)52-54(44,45)48-10-16-20(51-53(41,42)43)19(37)25(50-16)34-13-33-18-22(28)31-12-32-23(18)34/h12-16,19-21,25,35,37-38H,5-11H2,1-4H3,(H,29,36)(H,30,39)(H,44,45)(H,46,47)(H2,28,31,32)(H2,41,42,43)/t15-,16-,19-,20-,21+,25-/m1/s1
InChIKeyCFNPCSNXESBNGR-LYALRYAQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CC(C)CC(C(=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)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(O)CC(C)C
OpenEye OEToolkits 1.7.0CC(C)C[C@H](C(=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)O
CACTVS 3.370CC(C)C[CH](O)C(=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 3.370CC(C)C[C@@H](O)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
FormulaC27 H46 N7 O18 P3 S
NameS-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl ]oxy-hydroxy-phosphoryl]oxy-2-hydroxy-3,3-dimethyl-butanoyl]amino]propanoylamino]ethyl] (2R)-2-hydroxy-4-methyl-pentanethioate;
(R)-2-hydroxy-4-methylpentanoyl-CoA
ChEMBL
DrugBank
ZINCZINC000198017613
PDB chain3o3n Chain C Residue 410 [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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PDB3o3n Structural Basis for Reductive Radical Formation and Electron Recycling in (R)-2-Hydroxyisocaproyl-CoA Dehydratase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		N12 E55 N56 G60 K64 Y86 I116 M218 A219 I265 Y290 W294 M313 F314
Binding residue
(residue number reindexed from 1)		N9 E52 N53 G57 K61 Y83 I113 M215 A216 I262 Y287 W291 M310 F311
Annotation score4
Enzymatic activity
Enzyme Commision number 4.2.1.157: (R)-2-hydroxyisocaproyl-CoA dehydratase.
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0016836 hydro-lyase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006551 L-leucine metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3o3n, PDBe:3o3n, PDBj:3o3n
PDBsum3o3n
PubMed21366233
UniProtQ5U924|HADB_CLODI (R)-2-hydroxyisocaproyl-CoA dehydratase alpha subunit (Gene Name=hadB)

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