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 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
Ligand General Information  Top
Ligand Name adenosine diphosphate Ligand Info
Canonical SMILES C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
InChI 1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKey XTWYTFMLZFPYCI-KQYNXXCUSA-N
PubChem Compound ID 6022
Drug Binding Sites of Target  Top
PDB ID: 1UCN      X-ray structure of human nucleoside diphosphate kinase A complexed with ADP at 2 A resolution
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
PDB ID: 2HVD      Human nucleoside diphosphate kinase A complexed with ADP
Method X-ray diffraction Resolution 2.15 Å Mutation No [2]
PDB Sequence
ANCERTFIAI
11
KPDGVQRGLV
21
GEIIKRFEQK
31
GFRLVGLKFM
41
QASEDLLKEH
51

YVDLKDRPFF
61
AGLVKYMHSG
71
PVVAMVWEGL
81
NVVKTGRVML
91
GETNPADSKP
101

GTIRGDFCIQ
111
VGRNIIHGSD
121
SVESAEKEIG
131
LWFHPEELVD
141
YTSCAQNWIY
151

E
Residue
Distance (Å)
LYS12
2.200
TYR52
3.738
LEU55
3.465
PHE60
3.477
LEU64
3.458
TYR67
4.434
ARG88
3.111
THR94
2.290
Residue
Distance (Å)
ARG105
4.079
VAL112
3.675
GLY113
3.888
ASN115
3.081
ILE117
4.616
HIS118
4.116
GLY119
4.705
ASP121
4.840
PDB ID: 2HVE      S120G mutant of human nucleoside diphosphate kinase A complexed with ADP
Method X-ray diffraction Resolution 2.40 Å Mutation Yes [2]
PDB Sequence
ANCERTFIAI
11
KPDGVQRGLV
21
GEIIKRFEQK
31
GFRLVGLKFM
41
QASEDLLKEH
51

YVDLKDRPFF
61
AGLVKYMHSG
71
PVVAMVWEGL
81
NVVKTGRVML
91
GETNPADSKP
101

GTIRGDFCIQ
111
VGRNIIHGGD
121
SVESAEKEIG
131
LWFHPEELVD
141
YTSCAQNWIY
151

E
Residue
Distance (Å)
LYS12
2.563
TYR52
3.500
LEU55
3.632
PHE60
3.635
LEU64
3.552
TYR67
4.411
ARG88
3.209
THR94
2.203
Residue
Distance (Å)
ARG105
4.306
VAL112
3.640
GLY113
4.067
ASN115
3.171
ILE117
4.729
HIS118
4.202
GLY119
4.446
ASP121
4.753
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 Crystal structures of S120G mutant and wild type of human nucleoside diphosphate kinase A in complex with ADP. J Bioenerg Biomembr. 2006 Aug;38(3-4):261-4.

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