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 T30081 Target Info
Target Name Thymidine kinase 1 (TK1)
Synonyms Thymidine kinase, cytosolic
Target Type Successful Target
Gene Name TK1
Biochemical Class Kinase
UniProt ID
KITH_HUMAN
Ligand General Information  Top
Ligand Name 2'-deoxythymidine triphosphate Ligand Info
Canonical SMILES CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
InChI 1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKey NHVNXKFIZYSCEB-XLPZGREQSA-N
PubChem Compound ID 64968
Drug Binding Sites of Target  Top
PDB ID: 1W4R      Structure of a type II thymidine kinase with bound dTTP
Method X-ray diffraction Resolution 1.83 Å Mutation No [1]
PDB Sequence
RGQIQVILGP
27
MFSGKSTELM
37
RRVRRFQIAQ
47
YKCLVIKYAK
57
DTRYSSSFCT
67

HDRNTMEALP
77
ACLLRDVAQE
87
ALGVAVIGID
97
EGQFFPDIVE
107
FCEAMANAGK
117

TVIVAALDGT
127
FQRKPFGAIL
137
NLVPLAESVV
147
KLTAVCMECF
157
REAAYTKRLG
167

TEKEVEVIGG
177
ADKYHSVCRL
187
CYFK
Residue
Distance (Å)
PRO27
3.803
MET28
3.500
PHE29
2.911
SER30
3.400
GLY31
3.002
LYS32
2.538
SER33
3.195
THR34
4.745
ASP58
2.694
ARG60
3.246
SER63
4.440
ASP97
4.680
GLU98
3.440
GLN100
4.037
Residue
Distance (Å)
PHE101
3.281
LEU124
3.366
GLY126
4.190
THR127
3.461
PHE128
2.777
PHE133
3.515
THR163
3.703
ARG165
3.733
VAL172
2.729
GLU173
3.252
VAL174
2.840
ILE175
3.421
GLY176
3.271
TYR181
3.141
PDB ID: 2WVJ      Mutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Specificity from Thymidine towards the Nucleoside Analogue Azidothymidine
Method X-ray diffraction Resolution 2.20 Å Mutation Yes [2]
PDB Sequence
RGQIQVILGP
27
MFSGKSTELM
37
RRVRRFQIAQ
47
YKCLVIKYAK
57
DTRALPACLL
81

RDVAQEALGV
91
AVIGIDEGQF
101
FPDIVEFCEA
111
MANAGKTVIV
121
AALDGTFQRK
131

PFGAILNLVP
141
LAESVVKLTA
151
VCMECFREAA
161
YSKRLGTEKE
171
VEVIGGADKY
181

HSVCRLCYFK
191
Residue
Distance (Å)
PRO27
4.336
MET28
3.640
PHE29
3.908
SER30
3.594
GLY31
2.951
LYS32
2.648
SER33
2.732
THR34
4.271
ASP58
2.833
ARG60
3.520
ASP97
2.724
GLU98
3.399
GLN100
3.340
PHE101
3.545
Residue
Distance (Å)
ALA123
4.738
LEU124
3.196
GLY126
4.083
THR127
3.467
PHE128
2.851
PHE133
3.512
SER163
3.511
ARG165
3.738
VAL172
2.708
GLU173
3.515
VAL174
2.977
ILE175
3.393
GLY176
3.031
TYR181
3.234
PDB ID: 1XBT      Crystal Structure of Human Thymidine Kinase 1
Method X-ray diffraction Resolution 2.40 Å Mutation No [3]
PDB Sequence
RGQIQVILGP
27
MFSGKSTELM
37
RRVRRFQIAQ
47
YKCLVIKYAK
57
DTRALPACLL
81

RDVAQEALGV
91
AVIGIDEGQF
101
FPDIVEFCEA
111
MANAGKTVIV
121
AALDGTFQRK
131

PFGAILNLVP
141
LAESVVKLTA
151
VCMECFREAA
161
YTKRLGTEKE
171
VEVIGGADKY
181

HSVCRLCYFK
191
Residue
Distance (Å)
PRO27
3.931
MET28
3.594
PHE29
2.859
SER30
3.497
GLY31
3.116
LYS32
2.830
SER33
3.121
ASP58
2.739
ARG60
3.502
ASP97
4.701
GLU98
3.639
GLN100
4.029
PHE101
3.340
Residue
Distance (Å)
LEU124
3.205
GLY126
4.226
THR127
3.647
PHE128
3.029
PHE133
3.669
THR163
3.750
ARG165
3.526
VAL172
2.658
GLU173
3.456
VAL174
2.870
ILE175
3.489
GLY176
3.206
TYR181
3.173
References  Top
REF 1 Structure of a type II thymidine kinase with bound dTTP. FEBS Lett. 2005 Feb 28;579(6):1376-82.
REF 2 Comparative active-site mutation study of human and Caenorhabditis elegans thymidine kinase 1. FEBS J. 2012 May;279(10):1777-87.
REF 3 Structures of thymidine kinase 1 of human and mycoplasmic origin. Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):17970-5.

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