Structure of PDB 2gce Chain D Binding Site BS02

Receptor Information

>2gce Chain D (length=354) Species: 1773 (Mycobacterium tuberculosis)

AGPLSGLRVVELAGIGPGPHAAMILGDLGADVVRIDRPISRDAMLRNRRI
VTADLKSDQGLELALKLIAKADVLIEGYRPGVTERLGLGPEECAKVNDRL
IYARMTGWGQTGPRSQQAGHDINYISLNGILHAIGRGDERPVPPLNLVGD
FGGGSMFLLVGILAALWERQSSGKGQVVDAAMVDGSSVLIQMMWAMRATG
MWTDTRGANMLDGGAPYYDTYECADGRYVAVGAIEPQFYAAMLAGLGLDA
AELPPQNDRARWPELRALLTEAFASHDRDHWGAVFANSDACVTPVLAFGE
VHNEPHIIERNTFYEANGGWQPMPAPRFSRTASSQPRPPAATIDIEAVLT
DWDG

Ligand information

• Ligand ID: SFC
• InChI: InChI=1S/C34H52N7O17P3S/c1-19(2)14-21-6-8-22(9-7-21)20(3)33(46)62-13-12-36-24(42)10-11-37-31(45)28(44)34(4,5)16-55-61(52,53)58-60(50,51)54-15-23-27(57-59(47,48)49)26(43)32(56-23)41-18-40-25-29(35)38-17-39-30(25)41/h6-9,17-20,23,26-28,32,43-44H,10-16H2,1-5H3,(H8,35,36,37,38,39,42,45,47,48,49,50,51,52,53)/p+1/t20-,23+,26+,27+,28-,32+/m0/s1
• InChIKey: NXIKDQUQQHUCJH-MIXAKNBRSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)Cc1ccc(cc1)[C@H](C)C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)[n+]3c[nH]c4c3ncnc4N)O)OP(=O)(O)O)O
  CACTVS 3.341: CC(C)Cc1ccc(cc1)[C@H](C)C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O[P](O)(O)=O)[n+]3c[nH]c4c(N)ncnc34
  CACTVS 3.341: CC(C)Cc1ccc(cc1)[CH](C)C(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O[P](O)(O)=O)[n+]3c[nH]c4c(N)ncnc34
  ACDLabs 10.04: O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC([n+]2cnc1c2ncnc1N)C(O)C3OP(=O)(O)O)C(c4ccc(cc4)CC(C)C)C
  OpenEye OEToolkits 1.5.0: CC(C)Cc1ccc(cc1)C(C)C(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)[n+]3c[nH]c4c3ncnc4N)O)OP(=O)(O)O)O
• Formula: C34 H53 N7 O17 P3 S
• Name: (S)-IBUPROFENOYL-COENZYME A;
  [5-(6-AMINOPURIN-9-YL)-2-[[[[3-[2-(2-(S)-2-[4-(2-METHYLPROPYL)PHENYL] PROPANOYL)-SULFANYLETHYLCARBAMOYL ETHYLCARBAMOYL]-3-HYDROXY-2,2-DIMETHYL-PROPOXY]-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXYMETHYL]-4-HYDROXY-OXOLAN-3-YL]OXYPHOSPHONIC ACID
• ZINC: ZINC000263620816
• PDB chain: 2gce Chain D Residue 1754

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2gce 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
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): G17 R38 L61 K62 Y84 R85 V88 R91 L92 T112 A124 G125 H126 D127 Y130 N152 D156 M188
• Binding residue (residue number reindexed from 1): G16 R37 L55 K56 Y78 R79 V82 R85 L86 T106 A118 G119 H120 D121 Y124 N146 D150 M182
• Annotation score: 3
• Binding affinity: MOAD: Kd=24.5uM

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

External links

• PDB: RCSB:2gce, PDBe:2gce, PDBj:2gce
• PDBsum: 2gce
• PubMed: 17320106
• UniProt: O06543|AMACR_MYCTU Alpha-methylacyl-CoA racemase (Gene Name=mcr)