Structure of PDB 1rpn Chain D Binding Site BS02

Receptor Information
>1rpn Chain D (length=322) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRSALVTGITGQDGAYLAKLLLEKGYRVHGLVARRSSDTRWRLRELGIEG
DIQYEDGDMADACSVQRAVIKAQPQEVYNLAAQSFVGASWNQPVTTGVVD
GLGVTHLLEAIRQFSPETRFYQASTSEMFGLIQAERQDENTPFYPRSPYG
VAKLYGHWITVNYRESFGLHASSGILFNHESPLRGIEFVTRKVTDAVARI
KLGKQQELRLGNVDAKRDWGFAGDYVEAMWLMLQQDKADDYVVATGVTTT
VRDMCQIAFEHVGLDYRDFLKIDPAFFRPAEVDVLLGNPAKAQRVLGWKP
RTSLDELIRMMVEADLRRVSRE
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 chain1rpn Chain D Residue 1504 [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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PDB1rpn Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		G9 T11 G12 Q13 D14 R36 D59 M60 L81 A82 A83 S85 A124 S125 T126 Y150 K154 L177 N179 H180 R185
Binding residue
(residue number reindexed from 1)		G8 T10 G11 Q12 D13 R35 D58 M59 L80 A81 A82 S84 A123 S124 T125 Y149 K153 L176 N178 H179 R184
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T126 S127 E128 Y150 K154
Catalytic site (residue number reindexed from 1) T125 S126 E127 Y149 K153
Enzyme Commision number 4.2.1.47: GDP-mannose 4,6-dehydratase.
Gene Ontology
Molecular Function
GO:0008446 GDP-mannose 4,6-dehydratase activity
GO:0016829 lyase activity
GO:0070401 NADP+ binding
Biological Process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009243 O antigen biosynthetic process
GO:0019306 GDP-D-rhamnose biosynthetic process
GO:0019673 GDP-mannose metabolic process
GO:0042351 'de novo' GDP-L-fucose biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1rpn, PDBe:1rpn, PDBj:1rpn
PDBsum1rpn
PubMed14739333
UniProtQ51366|GM4D_PSEAE GDP-mannose 4,6-dehydratase (Gene Name=gmd)

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