Structure of PDB 1rpn Chain A Binding Site BS01

Receptor Information
>1rpn Chain A (length=321) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSALVTGITGQDGAYLAKLLLEKGYRVHGLVARRSSDTRWRLRELGIEGD
IQYEDGDMADACSVQRAVIKAQPQEVYNLAAQSFVGASWNQPVTTGVVDG
LGVTHLLEAIRQFSPETRFYQASTSEMFGLIQAERQDENTPFYPRSPYGV
AKLYGHWITVNYRESFGLHASSGILFNHESPLRGIEFVTRKVTDAVARIK
LGKQQELRLGNVDAKRDWGFAGDYVEAMWLMLQQDKADDYVVATGVTTTV
RDMCQIAFEHVGLDYRDFLKIDPAFFRPAEVDVLLGNPAKAQRVLGWKPR
TSLDELIRMMVEADLRRVSRE
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 A Residue 1501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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 A34 R36 D59 M60 L81 A82 A83 S85 V100 A124 S125 T126 Y150 K154 L177 N179 H180 R185
Binding residue
(residue number reindexed from 1)		G7 T9 G10 Q11 D12 A32 R34 D57 M58 L79 A80 A81 S83 V98 A122 S123 T124 Y148 K152 L175 N177 H178 R183
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T126 S127 E128 Y150 K154
Catalytic site (residue number reindexed from 1) T124 S125 E126 Y148 K152
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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