Structure of PDB 2hrm Chain A Binding Site BS01

Receptor Information
>2hrm Chain A (length=137) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MMKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTL
VPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMIS
VWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFD
Ligand information
Ligand IDUC5
InChIInChI=1S/C10H16N2O10P2/c13-6-3-9(12-2-1-8(14)11-10(12)15)22-7(6)4-21-24(19,20)5-23(16,17)18/h1-2,6-7,9,13H,3-5H2,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,9+/m0/s1
InChIKeyMYBNSHXDOWMNJH-LKEWCRSYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O)(CP(=O)(O)O)O)O
CACTVS 3.341O[CH]1C[CH](O[CH]1CO[P](O)(=O)C[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(CP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)C[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
FormulaC10 H16 N2 O10 P2
Name2'-DEOXY-5'-O-[(S)-HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]URIDINE
ChEMBLCHEMBL1236535
DrugBank
ZINC
PDB chain2hrm Chain A Residue 777 [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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PDB2hrm Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		N84 L88 I89 D90 Y93 M98
Binding residue
(residue number reindexed from 1)		N84 L88 I89 D90 Y93 M98
Annotation score2
Binding affinityMOAD: Kd=278.5uM
PDBbind-CN: -logKd/Ki=3.56,Kd=278.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) A29 R71 G73 I80 D90
Catalytic site (residue number reindexed from 1) A29 R71 G73 I80 D90
Enzyme Commision number 3.6.1.23: dUTP diphosphatase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004170 dUTP diphosphatase activity
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006226 dUMP biosynthetic process
GO:0009117 nucleotide metabolic process
GO:0046081 dUTP catabolic process
GO:0070207 protein homotrimerization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2hrm, PDBe:2hrm, PDBj:2hrm
PDBsum2hrm
PubMed17932923
UniProtP06968|DUT_ECOLI Deoxyuridine 5'-triphosphate nucleotidohydrolase (Gene Name=dut)

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