Target Binding Site Detail

Content Navigation (  All   None )                                      
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 1-Diphosinositol pentakisphosphate 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?/m1/s1
InChIKey UPHPWXPNZIOZJL-GCVPSNMTSA-N
PubChem Compound ID 127296
Drug Binding Sites of Target  Top
PDB ID: 6WOI      Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1-Diphosphoinositol pentakisphosphate, Mg, and Fluoride ion, presoaked with 1,5-IP8, Mg and Fluoride for 30 seconds
Method X-ray diffraction Resolution 1.50 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
3.231
LYS18
2.826
ARG20
2.811
SER38
4.850
SER39
2.640
SER40
2.507
ARG41
3.685
HIS42
4.587
ILE47
3.430
Residue
Distance (Å)
GLY50
3.036
GLY51
3.278
GLY52
2.796
GLU66
3.180
GLU70
2.796
ARG89
2.649
HIS91
3.723
ARG115
2.819
LYS133
2.731
PDB ID: 6WO9      Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1-diphosphoinositol pentakisphosphate (1-IP7) and Mg
Method X-ray diffraction Resolution 2.00 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
3.096
LYS18
2.810
ARG20
2.644
SER38
4.952
SER39
2.482
SER40
2.687
ARG41
3.406
HIS42
4.619
ILE47
3.640
Residue
Distance (Å)
GLY50
3.167
GLY51
3.415
GLY52
2.868
GLU66
3.592
GLU70
2.844
ARG89
2.775
HIS91
2.616
ARG115
2.847
LYS133
2.867
PDB ID: 6PCK      Crystal structure of human diphosphoinositol polyphosphate phosphohydrolase 1 in complex with 1-IP7
Method X-ray diffraction Resolution 1.20 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
2.800
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
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.

If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.