Structure of PDB 2bnd Chain B Binding Site BS01

Receptor Information
>2bnd Chain B (length=237) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NAKPVYKRILLKLSGEALQGTEFGIDASILDRMAQEIKELVELGIQVGVV
IGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARL
MSAIPLNAVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGI
EIEANVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAA
FTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain2bnd Chain B Residue 1242 [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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PDB2bnd Structure of Escherichia Coli Ump Kinase Differs from that of Other Nucleoside Monophosphate Kinases and Sheds New Light on Enzyme Regulation.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		K15 S17 G57 G58 R62 G63 D77 G80 M81 T138 N140 F143 T144 T145
Binding residue
(residue number reindexed from 1)		K12 S14 G53 G54 R58 G59 D73 G76 M77 T134 N136 F139 T140 T141
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.4.22: UMP kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0009041 UMP/dUMP kinase activity
GO:0016301 kinase activity
GO:0033862 UMP kinase activity
GO:0042802 identical protein binding
Biological Process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006225 UDP biosynthetic process
GO:0016310 phosphorylation
GO:0044210 'de novo' CTP biosynthetic process
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2bnd, PDBe:2bnd, PDBj:2bnd
PDBsum2bnd
PubMed15857829
UniProtP0A7E9|PYRH_ECOLI Uridylate kinase (Gene Name=pyrH)

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