Structure of PDB 8v9i Chain B Binding Site BS01

Receptor Information
>8v9i Chain B (length=576) Species: 1299 (Deinococcus radiodurans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDTPLLDQIHGPKDLKRLSREQLPALTEELRGEIVRVCSRGGLHLASSLG
AVDIITALHYVLDSPRDRILFDVGHQAYAHKILTGRRDQMADIKKEGGIS
GFTKVSESEHDAITVGHASTSLANALGMALARDAQGKDFHVAAVIGDGSL
TGGMALAALNTIGDMGRKMLIVLNDNEMSISENVGAMNKFMRGSVNPFAA
MGVRYVGPVDGHNVQELVWLLERLVDLDGPTILHIVTTKGKGLSYAEADP
IYWHGPAKFDPATGEYVPSSAYSWSAAFGEAVTEWAKTDPRTFVVTPAMR
EGSGLVEFSRVHPHRYLDVGIAEEVAVTTAAGMALQGMRPVVAIYSTFLQ
RAYDQVLHDVAIEHLNVTFCIDRAGIVGADGATHNGVFDLSFLRSIPGVR
IGLPKDAAELRGMLKYAQTHDGPFAIRYPRGNTAQVPAGTWPDLKWGEWE
RLKGGDDVVILAGGKALDYALKAAEDLPGVGVVNARFVKPLDEEMLREVG
GRARALITVEDNTVVGGFGGAVLEALNSMNLHPTVRVLGIPDEFQEHATA
ESVHARAGIDAPAIRTVLAELGVDVP
Ligand information
Ligand IDA1AAN
InChIInChI=1S/C27H36N7O13P3S/c1-17-23(10-12-46-50(43,44)47-49(40,41)42)51-26(33(17)15-20-14-29-18(2)30-24(20)28)27(3,37)48(38,39)45-11-9-21-16-34(32-31-21)22(25(35)36)13-19-7-5-4-6-8-19/h4-8,14,16,22,37H,9-13,15H2,1-3H3,(H6-,28,29,30,35,36,38,39,40,41,42,43,44)/p+1/t22-,27+/m1/s1
InChIKeySNCWGRJABBQATK-AMGIVPHBSA-O
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C](C)(O)[P](O)(=O)OCCc3cn(nn3)[CH](Cc4ccccc4)C(O)=O)c(N)n1
CACTVS 3.385Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@@](C)(O)[P](O)(=O)OCCc3cn(nn3)[C@H](Cc4ccccc4)C(O)=O)c(N)n1
OpenEye OEToolkits 2.0.7Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)(O)P(=O)(O)OCCc3cn(nn3)C(Cc4ccccc4)C(=O)O)CCOP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 2.0.7Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)P(=O)(O)OCCc3cn(nn3)[C@H](Cc4ccccc4)C(=O)O)CCOP(=O)(O)OP(=O)(O)O
ACDLabs 12.01OP(=O)(OCCc1cn(nn1)C(Cc1ccccc1)C(=O)O)C(C)(O)c1sc(CCOP(=O)(O)OP(=O)(O)O)c(C)[n+]1Cc1cnc(C)nc1N
FormulaC27 H37 N7 O13 P3 S
Name3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-[(S)-(2-{1-[(1R)-1-carboxy-2-phenylethyl]-1H-1,2,3-triazol-4-yl}ethoxy)(hydroxy)phosphoryl]-1-hydroxyethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
ChEMBL
DrugBank
ZINC
PDB chain8v9i Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8v9i Potent Inhibition of E. coli DXP Synthase by a gem -Diaryl Bisubstrate Analog.
Resolution1.981 Å
Binding residue
(original residue number in PDB)		G49 L50 H51 S54 H82 H124 A125 G153 D154 G155 S156 N183 M185 S186 I187 K289 H304 G305 M349 I371 E373 F398 R423 D430 H434 R480
Binding residue
(residue number reindexed from 1)		G42 L43 H44 S47 H75 H117 A118 G146 D147 G148 S149 N176 M178 S179 I180 K239 H254 G255 M299 I321 E323 F348 R373 D380 H384 R430
Annotation score1
Enzymatic activity
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:8v9i, PDBe:8v9i, PDBj:8v9i
PDBsum8v9i
PubMed38513073
UniProtQ9RUB5|DXS_DEIRA 1-deoxy-D-xylulose-5-phosphate synthase (Gene Name=dxs)

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