Structure of PDB 3dr4 Chain D Binding Site BS01

Receptor Information
>3dr4 Chain D (length=367) Species: 155892 (Caulobacter vibrioides) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRISVAAPRLDGNERDYVLECMDTTWISSVGRFIVEFEKAFADYCGVKHA
IACNNGTTALHLALVAMGIGPGDEVIVPSLTYIASANSVTYCGATPVLVD
NDPRTFNLDAAKLEALITPRTKAIMPVHLYGQICDMDPILEVARRHNLLV
IEDAAEAVGATYRGKKSGSLGDCATFSFFGNAIITTGEGGMITTNDDDLA
AKMRLLRGQGMDPNRRYWFPIVGFNYRMTNIQAAIGLAQLERVDEHLAAR
ERVVGWYEQKLARLGNRVTKPHVALTGRHVFWMYTVRLGEGLSTTRDQVI
KDLDALGIESRPVFHPMHIMPPYAHLATDDLKIAEACGVDGLNLPTHAGL
TEADIDRVIAALDQVLV
Ligand information
Ligand IDG4M
InChIInChI=1S/C24H36N7O19P3/c1-8-15(32)11(10(3-26-8)5-45-51(38,39)40)4-27-13-9(2)47-23(19(36)17(13)34)49-53(43,44)50-52(41,42)46-6-12-16(33)18(35)22(48-12)31-7-28-14-20(31)29-24(25)30-21(14)37/h3,7,9,12-13,16-19,22-23,27,32-36H,4-6H2,1-2H3,(H,41,42)(H,43,44)(H2,38,39,40)(H3,25,29,30,37)/t9-,12-,13-,16-,17+,18-,19+,22-,23-/m1/s1
InChIKeyBNJJFFPICXKOFM-VMLLIFSYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N)[CH](O)[CH](O)[CH]1NCc5c(O)c(C)ncc5CO[P](O)(O)=O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC2C(OC(C(C2O)O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4N=C(NC5=O)N)O)O)C)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2[C@H](O[C@@H]([C@H]([C@H]2O)O)O[P@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4N=C(NC5=O)N)O)O)C)O
CACTVS 3.341C[C@H]1O[C@H](O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)[C@@H](O)[C@@H]1NCc5c(O)c(C)ncc5CO[P](O)(O)=O
ACDLabs 10.04O=P(OC2OC(C(NCc1c(cnc(c1O)C)COP(=O)(O)O)C(O)C2O)C)(O)OP(=O)(O)OCC5OC(n3c4N=C(N)NC(=O)c4nc3)C(O)C5O
FormulaC24 H36 N7 O19 P3
Name[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate
ChEMBL
DrugBank
ZINCZINC000098208921
PDB chain3dr4 Chain C Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dr4 Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase
Resolution1.6 Å
Binding residue
(original residue number in PDB)		T29 W30 S32 R220 Y221 N229
Binding residue
(residue number reindexed from 1)		T25 W26 S28 R216 Y217 N225
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Y86 D157 E160 F183 A186 Y221 R231
Catalytic site (residue number reindexed from 1) Y82 D153 E156 F179 A182 Y217 R227
Enzyme Commision number 2.6.1.102: GDP-perosamine synthase.
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
GO:0102933 GDP-4-dehydro-6-deoxy-D-mannose-4-aminotransferase activity
Biological Process
GO:0000271 polysaccharide biosynthetic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009243 O antigen biosynthetic process

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dr4, PDBe:3dr4, PDBj:3dr4
PDBsum3dr4
PubMed18795799
UniProtQ9A9H3|GDPPS_CAUVC GDP-perosamine synthase (Gene Name=per)

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