Structure of PDB 2bnf Chain B Binding Site BS01

Receptor Information
>2bnf Chain B (length=236) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NAKPVYKRILLKLSGEALQGTEFGIDASILDRMAQEIKELVELGIQVGVV
IGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARL
MSAIPLNVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIE
IEANVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAF
TLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE
Ligand information
Ligand IDUTP
InChIInChI=1S/C9H15N2O15P3/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPGAVKCOVUIYSFO-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H15 N2 O15 P3
NameURIDINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL336296
DrugBankDB04005
ZINCZINC000003861755
PDB chain2bnf 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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PDB2bnf Structure of Escherichia Coli Ump Kinase Differs from that of Other Nucleoside Monophosphate Kinases and Sheds New Light on Enzyme Regulation.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		K15 S17 G18 G56 G58 R62 G63 D77 G80 M81 T138 N140 F143 T144 T145
Binding residue
(residue number reindexed from 1)		K12 S14 G15 G52 G54 R58 G59 D73 G76 M77 T133 N135 F138 T139 T140
Annotation score3
Binding affinityMOAD: ic50=65uM
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:2bnf, PDBe:2bnf, PDBj:2bnf
PDBsum2bnf
PubMed15857829
UniProtP0A7E9|PYRH_ECOLI Uridylate kinase (Gene Name=pyrH)

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