Structure of PDB 6ime Chain B Binding Site BS02

Receptor Information
>6ime Chain B (length=285) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFPQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPR
IPADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELG
IKWLSLYAFSTENWKRSPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVG
SRPRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIARE
VAAGRLNPERITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAY
AEYIFQDKLWPDYDRRDLWAACEEYASRTRRFGSA
Ligand information
Ligand IDGST
InChIInChI=1S/C10H20O6P2S/c1-9(2)5-4-6-10(3)7-8-19-18(14,15)16-17(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+
InChIKeyAKIXWSDUEPPMKM-JXMROGBWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCSP(=O)(O)OP(=O)(O)O)C)C
CACTVS 3.341CC(C)=CCCC(C)=CCS[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCS[P@](=O)(O)OP(=O)(O)O)C)C
CACTVS 3.341CC(C)=CCCC(/C)=C/CS[P@@](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(O)(OP(=O)(O)O)SC/C=C(/CC/C=C(\C)C)C
FormulaC10 H20 O6 P2 S
NameGERANYL S-THIOLODIPHOSPHATE;
S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE
ChEMBL
DrugBankDB04702
ZINC
PDB chain6ime Chain B Residue 306 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ime Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		M75 D76 G77 N78 G79 R80 R89 H93 G96 A119 R127 W271
Binding residue
(residue number reindexed from 1)		M64 D65 G66 N67 G68 R69 R78 H82 G85 A108 R116 W260
Annotation score2
Enzymatic activity
Enzyme Commision number 2.5.1.86: trans,polycis-decaprenyl diphosphate synthase.
2.5.1.87: ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific].
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004659 prenyltransferase activity
GO:0008834 di-trans,poly-cis-undecaprenyl-diphosphate synthase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0030145 manganese ion binding
GO:0033850 Z-farnesyl diphosphate synthase activity
GO:0045547 dehydrodolichyl diphosphate synthase activity
GO:0046872 metal ion binding
GO:0052923 all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity
Biological Process
GO:0016094 polyprenol biosynthetic process
Cellular Component
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ime, PDBe:6ime, PDBj:6ime
PDBsum6ime
PubMed30950820
UniProtP9WFF7|DPDS_MYCTU Decaprenyl diphosphate synthase (Gene Name=uppS)

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