Structure of PDB 6ouv Chain A Binding Site BS01

Receptor Information
>6ouv Chain A (length=595) Species: 1299 (Deinococcus radiodurans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDTPLLDQIHGPKDLKRLSREQLPALTEELRGEIVRVCSRGGLHLASSLG
AVDIITALHYVLDSPRDRILFDVGHQAYAHKILTGRRDQMADIKKEGGIS
GFTKVSESEHDAITVGHASTSLANALGMALARDAQGKDFHVAAVIGDGSL
TGGMALAALNTIGDMGRKMLIVLNDNEMSISENVGAMNKFMRGLQVQKWF
QAVEAVSKPSVNPFAAMGVRYVGPVDGHNVQELVWLLERLVDLDGPTILH
IVTTKGKGLSYAEADPIYWHGPAKFDPATGEYVPSSAYSWSAAFGEAVTE
WAKTDPRTFVVTPAMREGSGLVEFSRVHPHRYLDVGIAEEVAVTTAAGMA
LQGMRPVVAIYSTFLQRAYDQVLHDVAIEHLNVTFCIDRAGIVGADGATH
NGVFDLSFLRSIPGVRIGLPKDAAELRGMLKYAQTHDGPFAIRYPRGNTA
QVPAGTWPDLKWGEWERLKGGDDVVILAGGKALDYALKAAEDLPGVGVVN
ARFVKPLDEEMLREVGGRARALITVEDNTVVGGFGGAVLEALNSMNLHPT
VRVLGIPDEFQEHATAESVHARAGIDAPAIRTVLAELGVDVPIEV
Ligand information
Ligand IDTDK
InChIInChI=1S/C15H25N4O11P3S/c1-9-12(5-6-29-33(26,27)30-32(23,24)25)34-14(15(3,20)31(21,22)28-4)19(9)8-11-7-17-10(2)18-13(11)16/h7,20H,5-6,8H2,1-4H3,(H5-,16,17,18,21,22,23,24,25,26,27)/p+1/t15-/m0/s1
InChIKeyILGXNMPRCMTAOK-HNNXBMFYSA-O
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc([n+](c1C)Cc2cnc(nc2N)C)C(O)(P(=O)(OC)O)C
OpenEye OEToolkits 1.7.5Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)(O)P(=O)(O)OC)CCOP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.5Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)[P@@](=O)(O)OC)CCO[P@@](=O)(O)OP(=O)(O)O
CACTVS 3.385CO[P](O)(=O)[C](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
CACTVS 3.385CO[P](O)(=O)[C@](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
FormulaC15 H26 N4 O11 P3 S
Name3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM;
2-PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000016051991
PDB chain6ouv Chain A Residue 701 [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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PDB6ouv X-ray crystallography-based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate.
Resolution1.937 Å
Binding residue
(original residue number in PDB)		H51 S54 H82 H124 A125 G153 D154 G155 S156 N183 M185 S186 I187 K289 H304 M349 I371 E373 F398 D430 H434
Binding residue
(residue number reindexed from 1)		H44 S47 H75 H117 A118 G146 D147 G148 S149 N176 M178 S179 I180 K255 H270 M315 I337 E339 F364 D396 H400
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.55,Ki=2.8uM
Enzymatic activity
Catalytic site (original residue number in PDB) K289 H304 E373 R401
Catalytic site (residue number reindexed from 1) K255 H270 E339 R367
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:6ouv, PDBe:6ouv, PDBj:6ouv
PDBsum6ouv
PubMed31239351
UniProtQ9RUB5|DXS_DEIRA 1-deoxy-D-xylulose-5-phosphate synthase (Gene Name=dxs)

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