Structure of PDB 2o1x Chain A Binding Site BS02

Receptor Information
>2o1x Chain A (length=578) Species: 1299 (Deinococcus radiodurans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PGTSDTPLLDQIHGPKDLKRLSREQLPALTEELRGEIVRVCSRGGLHLAS
SLGAVDIITALHYVLDSPRDRILFDVGHQAYAHKILTGRRDQMADIKKEG
GISGFTKVSESEHDAITVGHASTSLTNALGMALARDAQGKDFHVAAVIGD
GSLTGGMALAALNTIGDMGRKMLIVLNDNEMSISENVGAMNKFMSVNPFA
AMGVRYVGPVDGHNVQELVWLLERLVDLDGPTILHIVTTKGKGLSYAEAD
PIYWHGPAKFDPATGEYVPSSAYSWSAAFGEAVTEWAKTDPRTFVVTPAM
REGSGLVEFSRVHPHRYLDVGIAEEVAVTTAAGMALQGMRPVVAIYSTFL
QRAYDQVLHDVAIEHLNVTFCIDRAGIVGADGATHNGVFDLSFLRSIPGV
RIGLPKDAAELRGMLKYAQTHDGPFAIRYPRGNTAQVPAGTWPDLKWGEW
ERLKGGDDVVILAGGKALDYALKAAEDLPGVGVVNARFVKPLDEEMLREV
GGRARALITVEDNTVVGGFGGAVLEALNSMNLHPTVRVLGIPDEFQEHAT
AESVHARAGIDAPAIRTVLAELGVDVPI
Ligand information
Ligand IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain2o1x Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2o1x Crystal Structure of 1-Deoxy-D-xylulose 5-Phosphate Synthase, a Crucial Enzyme for Isoprenoids Biosynthesis.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		S54 H82 A125 G153 D154 G155 S156 N183 M185 S186 I187 K289 M349 I371 E373 F398
Binding residue
(residue number reindexed from 1)		S50 H78 A121 G149 D150 G151 S152 N179 M181 S182 I183 K240 M300 I322 E324 F349
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K289 H304 E373 R401 H434
Catalytic site (residue number reindexed from 1) K240 H255 E324 R352 H385
Enzyme Commision number 2.2.1.7: 1-deoxy-D-xylulose-5-phosphate synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0008661 1-deoxy-D-xylulose-5-phosphate synthase activity
GO:0016740 transferase activity
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0009228 thiamine biosynthetic process
GO:0016114 terpenoid biosynthetic process
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
GO:0052865 1-deoxy-D-xylulose 5-phosphate biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2o1x, PDBe:2o1x, PDBj:2o1x
PDBsum2o1x
PubMed17135236
UniProtQ9RUB5|DXS_DEIRA 1-deoxy-D-xylulose-5-phosphate synthase (Gene Name=dxs)

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