Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T24334 Target Info
Target Name Bacterial Deoxyuridine triphosphate nucleotidohydrolase (Bact dut)
Synonyms Deoxyuridine triphosphate nucleotidohydrolase; Deoxyuridine 5'-triphosphate nucleotidohydrolase; DUTPase; DUTP pyrophosphatase of Escherichia coli; Bact dut
Target Type Literature-reported Target
Gene Name Bact dut
Biochemical Class Acid anhydrides hydrolase
UniProt ID
DUT_ECOLI
Ligand General Information  Top
Ligand Name Deoxyuridine-5'-Diphosphate Ligand Info
Canonical SMILES C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)OP(=O)(O)O)O
InChI 1S/C9H14N2O11P2/c12-5-3-8(11-2-1-7(13)10-9(11)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKey QHWZTVCCBMIIKE-SHYZEUOFSA-N
PubChem Compound ID 145729
Drug Binding Sites of Target  Top
PDB ID: 2HR6      Crystal structure of dUTPase in complex with substrate analogue dUDP and manganese
Method X-ray diffraction Resolution 1.84 Å Mutation No [1]
PDB Sequence
MMKKIDVKIL
10
DPRVGKEFPL
20
PTYATSGSAG
30
LDLRACLNDA
40
VELAPGDTTL
50

VPTGLAIHIA
60
DPSLAAMMLP
70
RSGLGHKHGI
80
VLGNLVGLID
90
SDYQGQLMIS
100

VWNRGQDSFT
110
IQPGERIAQM
120
IFVPVVQAEF
130
NLVEDFD
Residue
Distance (Å)
MET68
3.631
ASN84
2.996
GLY87
3.433
LEU88
3.348
ILE89
3.771
ASP90
2.616
Residue
Distance (Å)
TYR93
3.456
GLN96
3.796
LEU97
3.864
MET98
2.800
ILE99
4.929
SER100
4.824
PDB ID: 1DUD      DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE (D-UTPASE) COMPLEXED WITH THE SUBSTRATE ANALOGUE DEOXYURIDINE 5'-DIPHOSPHATE (D-UDP)
Method X-ray diffraction Resolution 2.30 Å Mutation No [2]
PDB Sequence
MMKKIDVKIL
10
DPRVGKEFPL
20
PTYATSGSAG
30
LDLRACLNDA
40
VELAPGDTTL
50

VPTGLAIHIA
60
DPSLAAMMLP
70
RSGLGHKHGI
80
VLGNLVGLID
90
SDYQGQLMIS
100

VWNRGQDSFT
110
IQPGERIAQM
120
IFVPVVQAEF
130
NLVEDF
Residue
Distance (Å)
MET68
3.337
ASN84
3.247
GLY87
3.675
LEU88
3.466
ILE89
3.632
ASP90
2.662
Residue
Distance (Å)
TYR93
3.383
GLN96
3.675
LEU97
3.857
MET98
2.746
ILE99
4.859
SER100
4.749
References  Top
REF 1 Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site. Proteins. 2008 Apr;71(1):308-19.
REF 2 Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP). Nat Struct Biol. 1996 Jun;3(6):532-8.

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