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Receptor Information

>3dr4 Chain B (length=366) Species: 155892 (Caulobacter vibrioides) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

RISVAAPRLDGNERDYVLECMDTTWISSVGRFIVEFEKAFADYCGVKHAI
ACNNGTTALHLALVAMGIGPGDEVIVPSLTYIASANSVTYCGATPVLVDN
DPRTFNLDAAKLEALITPRTKAIMPVHLYGQICDMDPILEVARRHNLLVI
EDAAEAVGATYRGKKSGSLGDCATFSFFGNAIITTGEGGMITTNDDDLAA
KMRLLRGQGMDPNRRYWFPIVGFNYRMTNIQAAIGLAQLERVDEHLAARE
RVVGWYEQKLARLGNRVTKPHVALTGRHVFWMYTVRLGEGLSTTRDQVIK
DLDALGIESRPVFHPMHIMPPYAHLATDDLKIAEACGVDGLNLPTHAGLT
EADIDRVIAALDQVLV

Ligand ID

G4M

InChI

InChI=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

InChIKey

BNJJFFPICXKOFM-VMLLIFSYSA-N

SMILES

Software	SMILES
CACTVS 3.341	C[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 1.5.0	Cc1c(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 1.5.0	Cc1c(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 3.341	C[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 10.04	O=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

Formula

C24 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

PDB chain

3dr4 Chain B Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3dr4 Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase
Resolution	1.6 Å
Binding residue (original residue number in PDB)	A10 P12 N59 G60 T61 Y86 D157 A159 E160 S181 F183 G184 N185 E313 R315 F318
Binding residue (residue number reindexed from 1)	A5 P7 N54 G55 T56 Y81 D152 A154 E155 S176 F178 G179 N180 E308 R310 F313
Annotation score	2

Catalytic site (original residue number in PDB)	Y86 D157 E160 F183 A186 Y221 R231
Catalytic site (residue number reindexed from 1)	Y81 D152 E155 F178 A181 Y216 R226
Enzyme Commision number	2.6.1.102: GDP-perosamine synthase.

	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

PDB	RCSB:3dr4, PDBe:3dr4, PDBj:3dr4
PDBsum	3dr4
PubMed	18795799
UniProt	Q9A9H3\|GDPPS_CAUVC GDP-perosamine synthase (Gene Name=per)

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Structure of PDB 3dr4 Chain B Binding Site BS02