Structure of PDB 5dul Chain D Binding Site BS01

Receptor Information
>5dul Chain D (length=387) Species: 632 (Yersinia pestis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKQLTILGSTGSIGNSTLSVVRANPELFKVTALVAGRNVREMAQQCLEFS
PRYAAMSDEHSAKSLRLLLAEQGSDTEVYSGETAACELAALDDVDQVMAA
IVGIAGLPSTLAAIRAGKQVLLANKESLITCGKLFMDEVKRSRAQLLPID
SEHNAIFQSLPERIQRQLGYSSLNENGVSRIILTGSGGPFRETPLSQFSD
VTPDQACRKISVDSATMMNKGLEYIEARWLFNASAEQIEVVLHPQSVIHS
MVRYHDGSILAQMGTPDMRTPIAHAMAYPMRVSSGVAPLDFCKVGALTFT
TPDYQRYPCLKLAIDACNAGQAATTALNAANEISVMAFLDSKIRFTDIEV
INRTVVEGLLLSEPTSVEEVLVIDRKARDVAAQVIAK
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 chain5dul Chain D Residue 701 [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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PDB5dul 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis in complex with NADPH .
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G8 T10 G11 S12 I13 A35 G36 R37 N38 S57 A100 I101 V102 A123 N124 K125
Binding residue
(residue number reindexed from 1)		G8 T10 G11 S12 I13 A35 G36 R37 N38 S57 A100 I101 V102 A123 N124 K125
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.267: 1-deoxy-D-xylulose-5-phosphate reductoisomerase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0030145 manganese ion binding
GO:0030604 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
GO:0046872 metal ion binding
GO:0070402 NADPH binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
GO:0051484 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5dul, PDBe:5dul, PDBj:5dul
PDBsum5dul
PubMed
UniProtQ8ZH62|DXR_YERPE 1-deoxy-D-xylulose 5-phosphate reductoisomerase (Gene Name=dxr)

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