Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T42533 Target Info
Target Name Nucleoside diphosphate kinase A (NM23-H1)
Synonyms nm23H1; Tumor metastatic processassociated protein; Tumor metastatic process-associated protein; NM23; NDPKA; NDP kinase A; NDK A; Metastasis inhibition factor nm23; Granzyme Aactivated DNase; Granzyme A-activated DNase; GAAD
Target Type Literature-reported Target
Gene Name NME1
Biochemical Class Kinase
UniProt ID
NDKA_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: adenosine diphosphate Ligand Info
Structure Description X-ray structure of human nucleoside diphosphate kinase A complexed with ADP at 2 A resolution PDB:1UCN
Method X-ray diffraction Resolution 2.00 Å Mutation Yes [1]
PDB Sequence
ANCERTFIAI
11
KPDGVQRGLV
21
GEIIKRFEQK
31
GFRLVGLKFM
41
QASEDLLKEH
51

YVDLKDRPWF
61
AGLVKYMHSG
71
PVVAMVWEGL
81
NVVKTGRVML
91
GETNPADSKP
101

GTIRGDFCIQ
111
VGRNIIGGSD
121
SVESAEKEIG
131
LWFHPEELVD
141
YTSCAQNWIY
151

E
Residue
Distance (Å)
LYS12
2.652
TYR52
3.732
LEU55
3.665
TRP60
3.268
LEU64
3.392
TYR67
4.631
ARG88
2.722
GLU93
4.739
THR94
2.883
Residue
Distance (Å)
ARG105
2.792
VAL112
3.586
GLY113
4.712
ASN115
3.049
ILE117
4.438
GLY118
4.396
GLY119
4.839
ASP121
3.339
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Ligand Name: 4-[5-(3-Methoxyphenyl)-3-(prop-2-yn-1-yl)imidazol-4-yl]phenyl sulfurofluoridate Ligand Info
Structure Description Structure of NME1 covalently conjugated to imidazole fluorosulfate PDB:5UI4
Method X-ray diffraction Resolution 2.75 Å Mutation No [2]
PDB Sequence
NCERTFIAIK
12
PDGVQRGLVG
22
EIIKRFEQKG
32
FRLVGLKFMQ
42
ASEDLLKEHY
52

VDLKDRPFFA
62
GLVKYMHSGP
72
VVAMVWEGLN
82
VVKTGRVMLG
92
ETNPADSKPG
102

TIRGDFCIQV
112
GRNIIHGSDS
122
VESAEKEIGL
132
WFHPEELVDY
142
TSCAQNWIY
Residue
Distance (Å)
LYS12
1.600
TYR52
3.326
LEU55
3.915
ARG58
4.606
PHE60
3.294
GLY63
3.306
LEU64
3.489
TYR67
4.079
Residue
Distance (Å)
THR94
3.759
ARG105
3.911
VAL112
3.375
GLY113
3.557
ARG114
3.904
ASN115
2.605
ILE117
3.712
HIS118
3.093
References  Top
REF 1 Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases. J Mol Biol. 2003 Sep 26;332(4):915-26.
REF 2 Inverse Drug Discovery Strategy To Identify Proteins That Are Targeted by Latent Electrophiles As Exemplified by Aryl Fluorosulfates. J Am Chem Soc. 2018 Jan 10;140(1):200-210.

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