Binding Site Information of Target

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Target 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
Drug Binding Sites of Target  Top
Ligand Name: Myo-inositol hexaphosphate Ligand Info
Structure Description Human Diphosphoinositol polyphosphate phosphohydrolase 1 PDB:2FVV
Method X-ray diffraction Resolution 1.25 Å Mutation No [1]
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
2.431
LYS18
2.668
ARG20
2.747
SER39
3.225
SER40
3.724
ARG41
3.069
ILE47
3.750
Residue
Distance (Å)
GLY51
4.986
GLY52
4.556
ASN86
4.987
ARG89
2.862
HIS91
2.626
ARG115
4.223
LYS133
2.664
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: (1R,2S,3R,4R,5S,6S)-4-hydroxy-2,3,5,6-tetrakis(phosphonooxy)cyclohexyl trihydrogen diphosphate Ligand Info
Structure Description Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 3-diphosphoinositol 1,2,4,5-tetrakisphosphate (3-PP-IP4), Mg and Fluoride ion PDB:7TN4
Method X-ray diffraction Resolution 1.85 Å Mutation No [2]
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
2.718
LYS18
2.691
ARG20
2.675
SER38
4.773
SER39
2.746
SER40
2.522
ARG41
3.030
HIS42
4.919
ILE47
3.254
Residue
Distance (Å)
GLY50
2.978
GLY51
3.234
GLY52
2.881
GLU66
3.095
GLU70
2.542
ARG89
3.933
ARG115
3.252
LYS133
2.897
Ligand Name: 4-diphospho-1D-myo-inositol pentakisphosphate Ligand Info
Structure Description Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 4-diphosphoinositol pentakisphosphate (4-IP7), Mg, and Fluoride ion PDB:6WOB
Method X-ray diffraction Resolution 1.45 Å Mutation No [3]
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
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .U71 or .U712 or .U713 or :3U71;style chemicals stick;color identity;select .A:10 or .A:18 or .A:20 or .A:38 or .A:39 or .A:40 or .A:41 or .A:42 or .A:47 or .A:50 or .A:51 or .A:52 or .A:66 or .A:70 or .A:89 or .A:91 or .A:115 or .A:133; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG10
2.802
LYS18
2.688
ARG20
2.834
SER38
4.757
SER39
2.615
SER40
2.635
ARG41
3.479
HIS42
4.607
ILE47
3.397
Residue
Distance (Å)
GLY50
2.937
GLY51
3.271
GLY52
2.890
GLU66
3.070
GLU70
2.653
ARG89
2.632
HIS91
2.959
ARG115
2.882
LYS133
2.918
Ligand Name: (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate Ligand Info
Structure Description Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 2-Diphosphoinositol pentakisphosphate (2-IP7), Mg, and Fluoride ion PDB:6WOA
Method X-ray diffraction Resolution 1.50 Å Mutation No [3]
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
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UEV or .UEV2 or .UEV3 or :3UEV;style chemicals stick;color identity;select .A:10 or .A:18 or .A:20 or .A:38 or .A:39 or .A:40 or .A:41 or .A:45 or .A:47 or .A:50 or .A:51 or .A:52 or .A:66 or .A:70 or .A:89 or .A:91 or .A:115 or .A:133 or .A:136; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG10
2.907
LYS18
2.641
ARG20
2.710
SER38
4.762
SER39
2.846
SER40
2.788
ARG41
4.459
ARG45
4.862
ILE47
3.554
GLY50
3.181
Residue
Distance (Å)
GLY51
3.352
GLY52
2.789
GLU66
3.402
GLU70
2.689
ARG89
3.042
HIS91
2.822
ARG115
3.310
LYS133
2.713
GLN136
4.757
Ligand Name: Methylenebisphosphonate Inositol Pentakisphosphate Ligand Info
Structure Description Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-methylenebisphosphonate inositol pentakisphosphate (5-PCP-IP5) PDB:6WOG
Method X-ray diffraction Resolution 1.50 Å Mutation No [3]
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
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5A3 or .5A32 or .5A33 or :35A3;style chemicals stick;color identity;select .A:38 or .A:39 or .A:40 or .A:41 or .A:42 or .A:45 or .A:47 or .A:70 or .A:89 or .A:115 or .A:132 or .A:133; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER38
4.675
SER39
2.656
SER40
2.761
ARG41
2.696
HIS42
2.626
ARG45
2.673
Residue
Distance (Å)
ILE47
3.647
GLU70
4.957
ARG89
2.684
ARG115
2.767
HIS132
4.052
LYS133
2.845
Ligand Name: 5-Diphospho-myo-inositol 1,3,4,6-tetrakisphosphate Ligand Info
Structure Description Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-diphosphoinositol 1,3,4,6-tetrakisphosphate (5-PP-IP4), Mg, and Fluoride ion PDB:6WO8
Method X-ray diffraction Resolution 1.70 Å Mutation No [3]
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
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .U6J or .U6J2 or .U6J3 or :3U6J;style chemicals stick;color identity;select .A:10 or .A:18 or .A:20 or .A:38 or .A:39 or .A:40 or .A:41 or .A:42 or .A:47 or .A:50 or .A:51 or .A:52 or .A:66 or .A:70 or .A:89 or .A:91 or .A:115 or .A:133; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG10
2.793
LYS18
2.591
ARG20
2.805
SER38
4.850
SER39
2.738
SER40
2.766
ARG41
3.420
HIS42
4.745
ILE47
3.444
Residue
Distance (Å)
GLY50
2.908
GLY51
3.182
GLY52
2.912
GLU66
3.069
GLU70
2.580
ARG89
2.778
HIS91
3.454
ARG115
2.962
LYS133
2.822
Ligand Name: {[(1r,3s,4s,5r,6s)-2,4,5,6-Tetrakis(Phosphonooxy)cyclohexane-1,3-Diyl]bis[oxy(Hydroxyphosphoryl)methanediyl]}bis(Phosphonic Acid) Ligand Info
Structure Description Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1,5-di-methylenebisphosphonate inositol tetrakisphosphate (1,5-PCP-IP4) PDB:6WOH
Method X-ray diffraction Resolution 1.70 Å Mutation No [3]
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
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4WZ or .4WZ2 or .4WZ3 or :34WZ;style chemicals stick;color identity;select .A:38 or .A:39 or .A:40 or .A:41 or .A:42 or .A:45 or .A:47 or .A:89 or .A:115 or .A:132 or .A:133; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER38
4.498
SER39
2.723
SER40
2.780
ARG41
2.684
HIS42
2.416
ARG45
2.667
Residue
Distance (Å)
ILE47
3.759
ARG89
3.014
ARG115
2.928
HIS132
3.942
LYS133
2.846
Ligand Name: 1-Diphosinositol pentakisphosphate Ligand Info
Structure Description Crystal structure of human diphosphoinositol polyphosphate phosphohydrolase 1 in complex with 1-IP7 PDB:6PCK
Method X-ray diffraction Resolution 1.20 Å Mutation No [4]
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
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .O81 or .O812 or .O813 or :3O81;style chemicals stick;color identity;select .A:10 or .A:18 or .A:20 or .A:38 or .A:39 or .A:40 or .A:41 or .A:42 or .A:47 or .A:50 or .A:51 or .A:52 or .A:66 or .A:70 or .A:89 or .A:91 or .A:115 or .A:133; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG10
2.800
LYS18
2.778
ARG20
2.806
SER38
4.586
SER39
2.523
SER40
2.621
ARG41
2.702
HIS42
4.537
ILE47
3.397
Residue
Distance (Å)
GLY50
2.824
GLY51
3.244
GLY52
2.852
GLU66
3.152
GLU70
2.611
ARG89
2.836
HIS91
3.418
ARG115
2.734
LYS133
2.810
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate Ligand Info
Structure Description Crystal structure of human diphosphoinositol polyphosphate phosphohydrolase 1 in complex with 5-IP7 PDB:6PCL
Method X-ray diffraction Resolution 1.30 Å Mutation No [4]
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
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I7P or .I7P2 or .I7P3 or :3I7P;style chemicals stick;color identity;select .A:10 or .A:18 or .A:20 or .A:38 or .A:39 or .A:40 or .A:41 or .A:42 or .A:47 or .A:50 or .A:51 or .A:52 or .A:66 or .A:70 or .A:89 or .A:91 or .A:115 or .A:133; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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
Click to View More Binding Site Information of This Target and Ligand Pair
References  Top
REF 1 Crystal structure of human diphosphoinositol phosphatase 1. Proteins. 2009 Oct;77(1):242-6.
REF 2 Structural and catalytic analyses of the InsP(6) kinase activities of higher plant ITPKs. FASEB J. 2022 Jul;36(7):e22380.
REF 3 New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1. FASEB J. 2021 Feb;35(2):e21275.
REF 4 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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