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 T26748 Target Info
Target Name Diphosphoinositol polyphosphate phosphohydrolase 2 (NUDT3)
Synonyms NUDT3; Diphosphoinositol polyphosphate phosphohydrolase; DIPP2
Target Type Literature-reported Target
Gene Name NUDT3
Biochemical Class Acid anhydrides hydrolase
UniProt ID
NUDT3_HUMAN
Ligand General Information  Top
Ligand Name (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate Ligand Info
Canonical SMILES C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
InChI 1S/C6H19O27P7/c7-34(8,9)27-1-2(28-35(10,11)12)4(30-37(16,17)18)6(32-40(25,26)33-39(22,23)24)5(31-38(19,20)21)3(1)29-36(13,14)15/h1-6H,(H,25,26)(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1?,2-,3+,4+,5-,6?
InChIKey UPHPWXPNZIOZJL-UYSNGIAKSA-N
PubChem Compound ID 443247
Drug Binding Sites of Target  Top
PDB ID: 6WOC      Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-diphosphoinositol pentakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 1min in the absence of Fluoride.
Method X-ray diffraction Resolution 1.35 Å Mutation No [1]
PDB Sequence
TRTYDGDGYK
18
KRAACLCFRS
28
ESEEEVLLVS
38
SSRHPDRWIV
48
PGGGMEPEEE
58

PSVAAVREVC
68
EEAGVKGTLG
78
RLVGIFENQE
88
RKHRTYVYVL
98
IVTEVLEDWE
108

DSVNIGRKRE
118
WFKIEDAIKV
128
LQYHKPVQAS
138
YFET
Residue
Distance (Å)
ARG10
3.043
LYS18
2.809
ARG20
2.809
SER38
4.868
SER39
2.722
SER40
2.633
ARG41
3.236
ILE47
3.463
GLY50
2.951
Residue
Distance (Å)
GLY51
3.325
GLY52
2.895
GLU66
3.033
GLU70
2.683
ARG89
2.779
HIS91
3.627
ARG115
3.014
LYS133
2.978
PDB ID: 6WO7      Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-Diphosphoinositol pentakisphosphate (5-IP7), Mg, and Fluoride ion
Method X-ray diffraction Resolution 1.40 Å Mutation No [1]
PDB Sequence
TRTYDGDGYK
18
KRAACLCFRS
28
ESEEEVLLVS
38
SSRHPDRWIV
48
PGGGMEPEEE
58

PSVAAVREVC
68
EEAGVKGTLG
78
RLVGIFENQE
88
RKHRTYVYVL
98
IVTEVLEDWE
108

DSVNIGRKRE
118
WFKIEDAIKV
128
LQYHKPVQAS
138
YFET
Residue
Distance (Å)
ARG10
2.800
LYS18
2.564
ARG20
2.790
SER38
4.805
SER39
2.694
SER40
2.664
ARG41
3.134
HIS42
4.864
ILE47
3.516
Residue
Distance (Å)
GLY50
3.013
GLY51
3.259
GLY52
3.009
GLU66
3.097
GLU70
2.814
ARG89
2.825
HIS91
3.663
ARG115
3.006
LYS133
2.863
PDB ID: 6PCL      Crystal structure of human diphosphoinositol polyphosphate phosphohydrolase 1 in complex with 5-IP7
Method X-ray diffraction Resolution 1.30 Å Mutation No [2]
PDB Sequence
QTRTYDGDGY
17
KKRAACLCFR
27
SESEEEVLLV
37
SSSRHPDRWI
47
VPGGGMEPEE
57

EPSVAAVREV
67
CEEAGVKGTL
77
GRLVGIFENQ
87
ERKHRTYVYV
97
LIVTEVLEDW
107

EDSVNIGRKR
117
EWFKIEDAIK
127
VLQYHKPVQA
137
SYFET
Residue
Distance (Å)
ARG10
2.803
LYS18
2.606
ARG20
2.833
SER38
4.807
SER39
2.657
SER40
2.633
ARG41
3.900
HIS42
4.556
ILE47
3.480
Residue
Distance (Å)
GLY50
3.054
GLY51
3.340
GLY52
2.911
GLU66
3.157
GLU70
2.698
ARG89
2.869
HIS91
3.647
ARG115
2.856
LYS133
2.924
References  Top
REF 1 New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1. FASEB J. 2021 Feb;35(2):e21275.
REF 2 Vip1 is a kinase and pyrophosphatase switch that regulates inositol diphosphate signaling. Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9356-9364.

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