Structure of PDB 6x3b Chain D Binding Site BS01

Receptor Information
>6x3b Chain D (length=292) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TQRLFVTGLSGFVGKHLQAYLAAAHTPWALLPVPHRYDLLEPDSLGDLWP
ELPDAVIHLAGQTYVPEAFRDPARTLQINLLGTLNLLQALKARGFSGTFL
YISSGDVYGQVAEAALPIHEELIPHPRNPYAVSKLAAESLCLQWGITEGW
RVLVARPFNHIGPGQKDSFVIASAARQIARMKQGLQANRLEVGDIDVSRD
FLDVQDVLSAYLRLLSHGEAGAVYNVCSGQEQKIRELIELLADIAQVELE
IVQDPQRRVRGSHARLHDATGWKPEITIKQSLRAILSDWESR
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain6x3b Chain D Residue 401 [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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PDB6x3b X-ray crystallographic structure of RMD, the reductase involved in GDP-d-rhamnose production
Resolution1.91 Å
Binding residue
(original residue number in PDB)		G9 S11 G12 F13 V14 D39 L40 L60 A61 G62 T64 Y131 K135 H161
Binding residue
(residue number reindexed from 1)		G8 S10 G11 F12 V13 D38 L39 L59 A60 G61 T63 Y130 K134 H160
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) S105 G106 D107 Y131 K135
Catalytic site (residue number reindexed from 1) S104 G105 D106 Y130 K134
Enzyme Commision number 1.1.1.281: GDP-4-dehydro-6-deoxy-D-mannose reductase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0033705 GDP-4-dehydro-6-deoxy-D-mannose reductase activity
GO:0070402 NADPH binding
Biological Process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009243 O antigen biosynthetic process
GO:0019306 GDP-D-rhamnose biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6x3b, PDBe:6x3b, PDBj:6x3b
PDBsum6x3b
PubMed
UniProtQ9HTB6|RMD_PSEAE GDP-6-deoxy-D-mannose reductase (Gene Name=rmd)

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