Structure of PDB 2gd2 Chain A Binding Site BS01

Receptor Information
>2gd2 Chain A (length=354) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGPLSGLRVVELAGIGPGPHAAMILGDLGADVVRIDRPISRDAMLRNRRI
VTADLKSDQGLELALKLIAKADVLIEGYRPGVTERLGLGPEECAKVNDRL
IYARMTGWGQTGPRSQQAGHDINYISLNGILHAIGRGDERPVPPLNLVGD
FGGGSMFLLVGILAALWERQSSGKGQVVDAAMVDGSSVLIQMMWAMRATG
MWTDTRGANMLDGGAPYYDTYECADGRYVAVGAIEPQFYAAMLAGLGLDA
AELPPQNDRARWPELRALLTEAFASHDRDHWGAVFANSDACVTPVLAFGE
VHNEPHIIERNTFYEANGGWQPMPAPRFSRTASSQPRPPAATIDIEAVLT
DWDG
Ligand information
Ligand IDCAA
InChIInChI=1S/C25H40N7O18P3S/c1-13(33)8-16(35)54-7-6-27-15(34)4-5-28-23(38)20(37)25(2,3)10-47-53(44,45)50-52(42,43)46-9-14-19(49-51(39,40)41)18(36)24(48-14)32-12-31-17-21(26)29-11-30-22(17)32/h11-12,14,18-20,24,36-37H,4-10H2,1-3H3,(H,27,34)(H,28,38)(H,42,43)(H,44,45)(H2,26,29,30)(H2,39,40,41)/t14-,18-,19-,20+,24-/m1/s1
InChIKeyOJFDKHTZOUZBOS-CITAKDKDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=O)CC(=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 3.341CC(=O)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 1.5.0CC(=O)CC(=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
OpenEye OEToolkits 1.5.0CC(=O)CC(=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(C)CC(=O)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
FormulaC25 H40 N7 O18 P3 S
NameACETOACETYL-COENZYME A
ChEMBL
DrugBankDB03059
ZINCZINC000096014521
PDB chain2gd2 Chain A Residue 1751 [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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PDB2gd2 The Catalysis of the 1,1-Proton Transfer by alpha-Methyl-acyl-CoA Racemase Is Coupled to a Movement of the Fatty Acyl Moiety Over a Hydrophobic, Methionine-rich Surface
Resolution1.7 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 A53 L55 K56 G77 Y78 R79 V82 R85 L86 A118 G119 H120 Y124 D150
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) G17 D127 D156 G219 G220
Catalytic site (residue number reindexed from 1) G16 D121 D150 G213 G214
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:2gd2, PDBe:2gd2, PDBj:2gd2
PDBsum2gd2
PubMed17320106
UniProtO06543|AMACR_MYCTU Alpha-methylacyl-CoA racemase (Gene Name=mcr)

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