Structure of PDB 2yim Chain B Binding Site BS01

Receptor Information
>2yim Chain B (length=355) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGPLSGLRVVELAGIGPGPHAAMILGDLGADVVRIDRPSISRDAMLRNRR
IVTADLKSDQGLELALKLIAKADVLIEGYRPGVTERLGLGPEECAKVNDR
LIYARMTGWGQTGPRSQQAGHDINYISLNGILHAIGRGDERPVPPLNLVG
DFGGGSMFLLVGILAALWERQSSGKGQVVDAAMVDGSSVLIQMMWAMRAT
GMWTDTRGANMLDGGAPYYDTYECADGRYVAVGAIEPQFYAAMLAGLGLD
AAELPPQNDRARWPELRALLTEAFASHDRDHWGAVFANSDACVTPVLAFG
EVHNEPHIIERNTFYEANGGWQPMPAPRFSRTASSQPRPPAATIDIEAVL
TDWDG
Ligand information
Ligand IDMC4
InChIInChI=1S/C26H42N7O18P3S/c1-13(14(2)34)25(39)55-8-7-28-16(35)5-6-29-23(38)20(37)26(3,4)10-48-54(45,46)51-53(43,44)47-9-15-19(50-52(40,41)42)18(36)24(49-15)33-12-32-17-21(27)30-11-31-22(17)33/h11-12,15,18-20,24,36-37,39H,5-10H2,1-4H3,(H,28,35)(H,29,38)(H,43,44)(H,45,46)(H2,27,30,31)(H2,40,41,42)/p-1/b25-13-/t15-,18-,19-,20+,24-/m1/s1
InChIKeyHJBMSIYWKRMJGR-LURNCBTNSA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1CC(=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)C(=O)C
OpenEye OEToolkits 1.6.1C/C(=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)/C(=O)C
CACTVS 3.352CC(=O)/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
CACTVS 3.352CC(=O)C(C)=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
FormulaC26 H41 N7 O18 P3 S
Name2-METHYLACETOACETYL COA
ChEMBL
DrugBank
ZINC
PDB chain2yim Chain B Residue 1363 [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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PDB2yim The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 A Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed Qm/Mm Calculations.
Resolution1.41 Å
Binding residue
(original residue number in PDB)		I16 R38 A59 L61 K62 G83 Y84 R85 V88 R91 L92 A124 G125 H126 Y130 D156
Binding residue
(residue number reindexed from 1)		I15 R37 A54 L56 K57 G78 Y79 R80 V83 R86 L87 A119 G120 H121 Y125 D151
Annotation score3
Binding affinityMOAD: Kd=120uM
Enzymatic activity
Catalytic site (original residue number in PDB) G17 D127 D156 G219 G220
Catalytic site (residue number reindexed from 1) G16 D122 D151 G214 G215
Enzyme Commision number 5.1.99.4: alpha-methylacyl-CoA racemase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008111 alpha-methylacyl-CoA racemase activity
GO:0016853 isomerase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0006629 lipid metabolic process
GO:0006637 acyl-CoA metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2yim, PDBe:2yim, PDBj:2yim
PDBsum2yim
PubMed22360758
UniProtO06543|AMACR_MYCTU Alpha-methylacyl-CoA racemase (Gene Name=mcr)

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