Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T98089 | Target Info | |||
| Target Name | Deoxycytidine kinase (DCK) | ||||
| Synonyms | dCK | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | DCK | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Uridine-5'-Diphosphate | Ligand Info | |||
| Canonical SMILES | C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O | ||||
| InChI | 1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 | ||||
| InChIKey | XCCTYIAWTASOJW-XVFCMESISA-N | ||||
| PubChem Compound ID | 6031 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 2A2Z Crystal Structure of human deoxycytidine kinase in complex with deoxycytidine and uridine diphosphate | ||||||
| Method | X-ray diffraction | Resolution | 3.02 Å | Mutation | No | [1] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLCEDWE49 VVPEPVARWC59 NVQSTNVLQM84 MYEKPERWSF 94 TFQTYACLSR104 IRAQLASLNG114 KEKPVLFFER128 SVYSDRYIFA138 SNLYESECMN 148 ETEWTIYQDW158 HDWMNNQFGQ168 SLELDGIIYL178 QATPETCLHR188 IYLRGRNEEQ 198 GIPLEYLEKL208 HYKHESWLLH218 RTLKTNFDYL228 QEVPILTLDV238 NEDFKDKYES 248 LVEKVKEFLS258 TL
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| PDB ID: 2ZI5 C4S dCK variant of dCK in complex with L-dA+UDP | ||||||
| Method | X-ray diffraction | Resolution | 1.77 Å | Mutation | Yes | [2] |
| PDB Sequence |
RIKKISIEGN
1029 IAAGKSTFVN1039 ILKQLSEDWE1049 VVPEPVARWK1076 NGGNVLQMMY1086 EKPERWSFTF 1096 QTYACLSRIR1106 AQLASLNAEK1121 PVLFFERSVY1131 SDRYIFASNL1141 YESESMNETE 1151 WTIYQDWHDW1161 MNNQFGQSLE1171 LDGIIYLQAT1181 PETCLHRIYL1191 RGRNEEQGIP 1201 LEYLEKLHYK1211 HESWLLHRTL1221 KTNFDYLQEV1231 PILTLDVNED1241 FKDKYESLVE 1251 KVKEFLSTL
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| PDB ID: 2ZI6 C4S dCK variant of dCK in complex with D-dA+UDP | ||||||
| Method | X-ray diffraction | Resolution | 1.77 Å | Mutation | Yes | [2] |
| PDB Sequence |
RIKKISIEGN
1029 IAAGKSTFVN1039 ILKQLSEDWE1049 VVPEPVARWG1078 GNVLQMMYEK1088 PERWSFTFQT 1098 YACLSRIRAQ1108 LASLNAEKPV1123 LFFERSVYSD1133 RYIFASNLYE1143 SESMNETEWT 1153 IYQDWHDWMN1163 NQFGQSLELD1173 GIIYLQATPE1183 TCLHRIYLRG1193 RNEEQGIPLE 1203 YLEKLHYKHE1213 SWLLHRTLKT1223 NFDYLQEVPI1233 LTLDVNEDFK1243 DKYESLVEKV 1253 KEFLSTL
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| PDB ID: 2ZIA C4S dCK variant of dCK in complex with cladribine+UDP | ||||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [3] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NVGGNVLQMM85 YEKPERWSFT 95 FQTYACLSRI105 RAQLASLNAE120 KPVLFFERSV130 YSDRYIFASN140 LYESESMNET 150 EWTIYQDWHD160 WMNNQFGQSL170 ELDGIIYLQA180 TPETCLHRIY190 LRGRNEEQGI 200 PLEYLEKLHY210 KHESWLLHRT220 LKTNFDYLQE230 VPILTLDVNE240 DFKDKYESLV 250 EKVKEFLSTL260
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 3QEO S74E-R104M-D133A dCK variant in complex with L-deoxythymidine and UDP | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [4] |
| PDB Sequence |
TRIKKISIEG
28 NIAAGKSTFV38 NILKQLSEDW48 EVVPEPVARW58 SNVELTMEQK76 NGGNVLQMMY 86 EKPERWSFTF96 QTYACLSMIR106 AQLASLNGKL116 KDAEKPVLFF126 ERSVYSARYI 136 FASNLYESES146 MNETEWTIYQ156 DWHDWMNNQF166 GQSLELDGII176 YLQATPETCL 186 HRIYLRGRNE196 EQGIPLEYLE206 KLHYKHESWL216 LHRTLKTNFD226 YLQEVPILTL 236 DVNEDFKDKY246 ESLVEKVKEF256 LSTL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:37 or .A:127 or .A:188 or .A:191 or .A:192 or .A:238 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 2ZI7 C4S dCK variant of dCK in complex with D-dG+UDP | ||||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | Yes | [3] |
| PDB Sequence |
IKKISIEGNI
30 AAGKSTFVNI40 LKQLSEDWEV50 VPEPVARWSN60 VNGGNVLQMM85 YEKPERWSFT 95 FQTYACLSRI105 RAQLASLNKP122 VLFFERSVYS132 DRYIFASNLY142 ESESMNETEW 152 TIYQDWHDWM162 NNQFGQSLEL172 DGIIYLQATP182 ETCLHRIYLR192 GRNEEQGIPL 202 EYLEKLHYKH212 ESWLLHRTVP232 ILTLDVNEDF242 KDKYESLVEK252 VKEFLSTL |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .B:29 or .B:30 or .B:31 or .B:32 or .B:33 or .B:34 or .B:35 or .B:36 or .B:37 or .B:127 or .B:188 or .B:191 or .B:192 or .B:194 or .B:240 or .B:241 or .B:242 or .B:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 3QEN S74E dCK in complex with 5-bromodeoxycytidine and UDP | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [4] |
| PDB Sequence |
TRIKKISIEG
28 NIAAGKSTFV38 NILKQLSEDW48 EVVPEPVARW58 SNVQSELTME74 QKNGGNVLQM 84 MYEKPERWSF94 TFQTYACLSR104 IRAQLASLNG114 KLKDAEKPVL124 FFERSVYSDR 134 YIFASNLYES144 ESMNETEWTI154 YQDWHDWMNN164 QFGQSLELDG174 IIYLQATPET 184 CLHRIYLRGR194 NEEQGIPLEY204 LEKLHYKHES214 WLLHRTLKTN224 FDYLQEVPIL 234 TLDVNEDFKD244 KYESLVEKVK254 EFLSTL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:128 or .A:188 or .A:191 or .A:192 or .A:238 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 3MJR Human dCK complex with Acyclic Nucleoside | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [5] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NLTMSQKNGG79 NVLQMMYEKP 89 ERWSFTFQTY99 ACLSRIRAQL109 ASLNGKLKDA119 EKPVLFFERS129 VYSDRYIFAS 139 NLYESESMNE149 TEWTIYQDWH159 DWMNNQFGSL170 ELDGIIYLQA180 TPETCLHRIY 190 LRGRNEEQGI200 PLEYLEKLHY210 KHESWLLHRT220 LKTNFDYLQE230 VPILTLDVNE 240 DFKDKYESLV250 EKVKEFLSTL260
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 3QEJ S74E-dCK mutant in complex with UDP | ||||||
| Method | X-ray diffraction | Resolution | 2.49 Å | Mutation | Yes | [4] |
| PDB Sequence |
TRIKKISIEG
28 NIAAGKSTFV38 NILKQLSEDW48 EVVPEPVARW58 SNVELTMEQK76 NGGNVLQMMY 86 EKPERWSFTF96 QTYACLSRIR106 AQLASLNGKL116 KDAEKPVLFF126 ERSVYSDRYI 136 FASNLYESES146 MNETEWTIYQ156 DWHDWMNNQF166 GQSLELDGII176 YLQATPETCL 186 HRIYLRGRNE196 EQGIPLEYLE206 KLHYKHESWL216 LHRTLKTNFD226 YLQEVPILTL 236 DVNEDFKDKY246 ESLVEKVKEF256 LSTL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:37 or .A:127 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4Q1E Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 10 {2-{[(1R/S)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-methyl-1,3-thiazol 4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine} | ||||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | Yes | [6] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NLTMEQKNGG79 NVLQMMYEKP 89 ERWSFTFQTY99 ACLSRIRAQL109 ASLNGKLKDA119 EKPVLFFERS129 VYSDRYIFAS 139 NLYESESMNE149 TEWTIYQDWH159 DWMNNQFGQS169 LELDGIIYLQ179 ATPETCLHRI 189 YLRGRNEEQG199 IPLEYLEKLH209 YKHESWLLHR219 TLKTNFDYLQ229 EVPILTLDVN 239 EDFKDKYESL249 VEKVKEFLST259 L
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:37 or .A:127 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4JLK Human dCK C4S-S74E mutant in complex with UDP and the F2.2.1 inhibitoR (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-5-METHYL-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE) | ||||||
| Method | X-ray diffraction | Resolution | 1.89 Å | Mutation | Yes | [7] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NLTMEQKNGG79 NVLQMMYEKP 89 ERWSFTFQTY99 ACLSRIRAQL109 ASLNGKLKDA119 EKPVLFFERS129 VYSDRYIFAS 139 NLYESESMNE149 TEWTIYQDWH159 DWMNNGQSLE171 LDGIIYLQAT181 PETCLHRIYL 191 RGRNEEQGIP201 LEYLEKLHYK211 HESWLLHRTL221 KTNFDYLQEV231 PILTLDVNED 241 FKDKYESLVE251 KVKEFLSTL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4Q1A Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 6 {2-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethanol} | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [6] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 LTMEQKNGGN80 VLQMMYEKPE 90 RWSFTFQTYA100 CLSRIRAQLA110 SLNGKLKDAE120 KPVLFFERSV130 YSDRYIFASN 140 LYESESMNET150 EWTIYQDWHD160 WMNNQFGQSL170 ELDGIIYLQA180 TPETCLHRIY 190 LRGRNEEQGI200 PLEYLEKLHY210 KHESWLLHRT220 LKTNFDYLQE230 VPILTLDVNE 240 DFKDKYESLV250 EKVKEFLSTL260
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:238 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4L5B Human dCK C4S-S74E mutant in complex with UDP and the DI-43 inhibitor | ||||||
| Method | X-ray diffraction | Resolution | 1.94 Å | Mutation | Yes | [7] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NLTMEQKNGG79 NVLQMMYEKP 89 ERWSFTFQTY99 ACLSRIRAQL109 ASLNGKLKDA119 EKPVLFFERS129 VYSDRYIFAS 139 NLYESESMNE149 TEWTIYQDWH159 DWMNNQFGQS169 LELDGIIYLQ179 ATPETCLHRI 189 YLRGRNEEQG199 IPLEYLEKLH209 YKHESWLLHR219 TLKTNFDYLQ229 EVPILTLDVN 239 EDFKDKYESL249 VEKVKEFLST259 L
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:189 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4JLJ Human dCK C4S-S74E mutant in complex with UDP and the F2.1.1 inhibitor (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE) | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [8] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NELTMEQKNG78 GNVLQMMYEK 88 PERWSFTFQT98 YACLSRIRAQ108 LASLNGKLKD118 AEKPVLFFER128 SVYSDRYIFA 138 SNLYESESMN148 ETEWTIYQDW158 HDWMNNQFGQ168 SLELDGIIYL178 QATPETCLHR 188 IYLRGRNEEQ198 GIPLEYLEKL208 HYKHESWLLH218 RTLKTNFDYL228 QEVPILTLDV 238 NEDFKDKYES248 LVEKVKEFLS258 TL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:238 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4Q18 Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 4 [1-[5-(4-{[(2,6-diaminopyrimidin-4-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]-2-methylpropan-2-ol] | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [6] |
| PDB Sequence |
IKKISIEGNI
30 AAGKSTFVNI40 LKQLSEDWEV50 VPEPVARWSN60 LTMEQKNGGN80 VLQMMYEKPE 90 RWSFTFQTYA100 CLSRIRAQLA110 SLNGKLKDAE120 KPVLFFERSV130 YSDRYIFASN 140 LYESESMNET150 EWTIYQDWHD160 WMNNQFGQSL170 ELDGIIYLQA180 TPETCLHRIY 190 LRGRNEEQGI200 PLEYLEKLHY210 KHESWLLHRT220 LKTNFDYLQE230 VPILTLDVNE 240 DFKDKYESLV250 EKVKEFLSTL260
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:37 or .A:127 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4Q1C Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 8 {2,2'-[{4-[(2R)-4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-2,3-dihydro-1,3-thiazol-2-yl]benzene-1,2-diyl}bis(oxy)]diethanol} | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [6] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 LTMEQKNGGN80 VLQMMYEKPE 90 RWSFTFQTYA100 CLSRIRAQLA110 SLNGKLKDAE120 KPVLFFERSV130 YSDRYIFASN 140 LYESESMNET150 EWTIYQDWHD160 WMNNQFGQSL170 ELDGIIYLQA180 TPETCLHRIY 190 LRGRNEEQGI200 PLEYLEKLHY210 KHESWLLHRT220 LKTNFDYLQE230 VPILTLDVNE 240 DFKDKYESLV250 EKVKEFLSTL260
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4Q1D Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 9 {2-{[(1R)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-propyl-1,3-thiazol-4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine} | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [6] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NLTMEQKNGG79 NVLQMMYEKP 89 ERWSFTFQTY99 ACLSRIRAQL109 ASLNGKLKDA119 EKPVLFFERS129 VYSDRYIFAS 139 NLYESESMNE149 TEWTIYQDWH159 DWMNNQFGQS169 LELDGIIYLQ179 ATPETCLHRI 189 YLRGRNEEQG199 IPLEYLEKLH209 YKHESWLLHR219 TLKTNFDYLQ229 EVPILTLDVN 239 EDFKDKYESL249 VEKVKEFLST259 L
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:238 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4KCG Human dCK C4S-S74E mutant in complex with UDP and the DI-39 inhibitor | ||||||
| Method | X-ray diffraction | Resolution | 2.09 Å | Mutation | Yes | [9] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NTMEQKNGGN80 VLQMMYEKPE 90 RWSFTFQTYA100 CLSRIRAQLA110 SLNGKLKDAE120 KPVLFFERSV130 YSDRYIFASN 140 LYESESMNET150 EWTIYQDWHD160 WMNNQFGQSL170 ELDGIIYLQA180 TPETCLHRIY 190 LRGRNEEQGI200 PLEYLEKLHY210 KHESWLLHRT220 LKTNFDYLQE230 VPILTLDVNE 240 DFKDKYESLV250 EKVKEFLSTL260
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4Q19 Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 5 {5-(4-{[(4,6-DIAMINOPYRIMIDIN-2-YL)SULFANYL]METHYL}-5-PROPYL-1,3-THIAZOL-2-YL)-2-METHOXYPHENOL} | ||||||
| Method | X-ray diffraction | Resolution | 2.09 Å | Mutation | Yes | [6] |
| PDB Sequence |
IKKISIEGNI
30 AAGKSTFVNI40 LKQLSEDWEV50 VPEPVARWSL71 TMEQKNGGNV81 LQMMYEKPER 91 WSFTFQTYAC101 LSRIRAQLAS111 LGKLKDAEKP122 VLFFERSVYS132 DRYIFASNLY 142 ESESMNETEW152 TIYQDWHDWM162 NNQFGQSLEL172 DGIIYLQATP182 ETCLHRIYLR 192 GRNEEQGIPL202 EYLEKLHYKH212 ESWLLHRTLK222 TNFDYLQEVP232 ILTLDVNEDF 242 KDKYESLVEK252 VKEFLSTL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:128 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4Q1F Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 12R {N-{2-[5-(4-{(1R)-1-[(4,6-diaminopyrimidin-2-yl)sulfanyl]ethyl}-5-methyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethyl}methanesulfonamide} | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | Yes | [6] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NLTMEQKNGG79 NVLQMMYEKP 89 ERWSFTFQTY99 ACLSRIRAQL109 ASLNGKLKDA119 EKPVLFFERS129 VYSDRYIFAS 139 NLYESESMNE149 TEWTIYQDWH159 DWMNNQFGQS169 LELDGIIYLQ179 ATPETCLHRI 189 YLRGRNEEQG199 IPLEYLEKLH209 YKHESWLLHR219 TLKTNFDYLQ229 EVPILTLDVN 239 EDFKDKYESL249 VEKVKEFLST259 L
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:238 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4JLN Human dCK C4S-S74E mutant in complex with UDP and the F2.4.1 inhibitor (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-5-PROPYL-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE) | ||||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | Yes | [8] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NELTMEQKNG78 GNVLQMMYEK 88 PERWSFTFQT98 YACLSRIRAQ108 LASLNGKLKD118 AEKPVLFFER128 SVYSDRYIFA 138 SNLYESESMN148 ETEWTIYQDW158 HDWMNNQFGQ168 SLELDGIIYL178 QATPETCLHR 188 IYLRGRNEEQ198 GIPLEYLEKL208 HYKHESWLLH218 RTLKTNFDYL228 QEVPILTLDV 238 NEDFKDKYES248 LVEKVKEFLS258 TL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:37 or .A:127 or .A:188 or .A:191 or .A:192 or .A:238 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4Q1B Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 7 {N-(2-(3-(4-(((4,6-diaminopyrimidin-2-yl)thio)methyl)-5-propylthiazol-2-yl)phenoxy)ethyl)methanesulfonamide} | ||||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | Yes | [6] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 TMEQKNGGNV81 LQMMYEKPER 91 WSFTFQTYAC101 LSRIRAQLAS111 LNGKLKDAEK121 PVLFFERSVY131 SDRYIFASNL 141 YESESMNETE151 WTIYQDWHDW161 MNNQFGQSLE171 LDGIIYLQAT181 PETCLHRIYL 191 RGRNEEQGIP201 LEYLEKLHYK211 HESWLLHRTL221 KTNFDYLQEV231 PILTLDVNED 241 FKDKYESLVE251 KVKEFLSTL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4JLM Human dCK C4S-S74E mutant in complex with UDP and the F2.3.1 inhibitor (2-[({5-ETHYL-2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE) | ||||||
| Method | X-ray diffraction | Resolution | 2.18 Å | Mutation | Yes | [8] |
| PDB Sequence |
TRIKKISIEG
28 NIAAGKSTFV38 NILKQLSEDW48 EVVPEPVARW58 SNELTMEQKN77 GGNVLQMMYE 87 KPERWSFTFQ97 TYACLSRIRA107 QLASLNGKLK117 DAEKPVLFFE127 RSVYSDRYIF 137 ASNLYESESM147 NETEWTIYQD157 WHDWMNNQFG167 QSLELDGIIY177 LQATPETCLH 187 RIYLRGRNEE197 QGIPLEYLEK207 LHYKHESWLL217 HRTLKTNFDY227 LQEVPILTLD 237 VNEDFKDKYE247 SLVEKVKEFL257 STL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:37 or .A:127 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 2QRN Human Deoxycytidine kinase dCMP, UDP, Mg ion product complex | ||||||
| Method | X-ray diffraction | Resolution | 3.40 Å | Mutation | No | [10] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLCEDWE49 VVPEPVARWC59 NVQSNGGNVL82 QMMYEKPERW 92 SFTFQTYACL102 SRIRAQLASL112 NGKLKDAEKP122 VLFFERSVYS132 DRYIFASNLY 142 ESECMNETEW152 TIYQDWHDWM162 NNQFGQSLEL172 DGIIYLQATP182 ETCLHRIYLR 192 GRNEEQGIPL202 EYLEKLHYKH212 ESWLLHRTLK222 TNFDYLQEVP232 ILTLDVNEDF 242 KDKYESLVEK252 VKEFLSTL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:194 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 2QRO Human Deoxycytidine kinase dAMP, UDP, Mg ion product complex | ||||||
| Method | X-ray diffraction | Resolution | 3.45 Å | Mutation | No | [10] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLCEDWE49 VVPEPVARWC59 NVQSNGGNVL82 QMMYEKPERW 92 SFTFQTYACL102 SRIRAQLASL112 NGKLKDAEKP122 VLFFERSVYS132 DRYIFASNLY 142 ESECMNETEW152 TIYQDWHDWM162 NNQFGQSLEL172 DGIIYLQATP182 ETCLHRIYLR 192 GRNEEQGIPL202 EYLEKLHYKH212 ESWLLHRTLK222 TNFDYLQEVP232 ILTLDVNEDF 242 KDKYESLVEK252 VKEFLSTL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:128 or .A:188 or .A:191 or .A:192 or .A:194 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 5MQJ Crystal structure of dCK mutant C3S | ||||||
| Method | X-ray diffraction | Resolution | 3.70 Å | Mutation | Yes | [11] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NVQSTQDENG78 GNVLQMMYEK 88 PERWSFTFQT98 YACLSRIRAQ108 LASLNGKLKD118 AEKPVLFFER128 SVYSDRYIFA 138 SNLYESECMN148 ETEWTIYQDW158 HDWMNNQFGQ168 SLELDGIIYL178 QATPETCLHR 188 IYLRGRNEEQ198 GIPLEYLEKL208 HYKHESWLLH218 RTLKTNFDYL228 QEVPILTLDV 238 NEDFKDKYES248 LVEKVKEFLS258 TL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 5MQT Crystal structure of dCK mutant C3S in complex with imatinib and UDP | ||||||
| Method | X-ray diffraction | Resolution | 3.20 Å | Mutation | Yes | [11] |
| PDB Sequence |
RIKKISIEGN
29 IAAGKSTFVN39 ILKQLSEDWE49 VVPEPVARWS59 NTMSQKNGGN80 VLQMMYEKPE 90 RWSFTFQTYA100 CLSRIRAQLA110 SLNGKLKDAE120 KPVLFFERSV130 YSDRYIFASN 140 LYESECMNET150 EWTIYQDWHD160 WMNNQFGQSL170 ELDGIIYLQA180 TPETCLHRIY 190 LRGRNEEQGI200 PLEYLEKLHY210 KHESWLLHRT220 LKTNFDYLQE230 VPILTLDVNE 240 DFKDKYESLV250 EKVKEFLSTL260
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:240 or .A:241 or .A:242 or .A:243; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 5MQL Crystal structure of dCK mutant C3S in complex with masitinib and UDP | ||||||
| Method | X-ray diffraction | Resolution | 3.25 Å | Mutation | Yes | [11] |
| PDB Sequence |
TRIKKISIEG
28 NIAAGKSTFV38 NILKQLSEDW48 EVVPEPVARW58 SNTMSQKNGG79 NVLQMMYEKP 89 ERWSFTFQTY99 ACLSRIRAQL109 ASLNGKLKDA119 EKPVLFFERS129 VYSDRYIFAS 139 NLYESECMNE149 TEWTIYQDWH159 DWMNNQFGQS169 LELDGIIYLQ179 ATPETCLHRI 189 YLRGRNEEQG199 IPLEYLEKLH209 YKHESWLLHR219 TLKTNFDYLQ229 EVPILTLDVN 239 EDFKDKYESL249 VEKVKEFLST259 L
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .A:29 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:36 or .A:127 or .A:188 or .A:191 or .A:192 or .A:238 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural basis for the preference of UTP over ATP in human deoxycytidine kinase: illuminating the role of main-chain reorganization. Biochemistry. 2006 Jan 17;45(2):452-61. | ||||
| REF 2 | Structural basis for substrate promiscuity of dCK. J Mol Biol. 2008 May 2;378(3):607-21. | ||||
| REF 3 | Elucidation of different binding modes of purine nucleosides to human deoxycytidine kinase. J Med Chem. 2008 Jul 24;51(14):4219-25. | ||||
| REF 4 | Post-translational phosphorylation of serine 74 of human deoxycytidine kinase favors the enzyme adopting the open conformation making it competent for nucleoside binding and release. Biochemistry. 2011 Apr 12;50(14):2870-80. | ||||
| REF 5 | The sugar ring of the nucleoside is required for productive substrate positioning in the active site of human deoxycytidine kinase (dCK): implications for the development of dCK-activated acyclic guanine analogues. J Med Chem. 2010 Aug 12;53(15):5792-800. | ||||
| REF 6 | Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability. J Med Chem. 2014 Nov 26;57(22):9480-94. | ||||
| REF 7 | Development of new deoxycytidine kinase inhibitors and noninvasive in vivo evaluation using positron emission tomography. J Med Chem. 2013 Sep 12;56(17):6696-708. | ||||
| REF 8 | Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules. Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):68-78. | ||||
| REF 9 | Co-targeting of convergent nucleotide biosynthetic pathways for leukemia eradication. J Exp Med. 2014 Mar 10;211(3):473-86. | ||||
| REF 10 | Structures of human deoxycytidine kinase product complexes. Acta Crystallogr D Biol Crystallogr. 2007 Dec;63(Pt 12):1201-7. | ||||
| REF 11 | Dual protein kinase and nucleoside kinase modulators for rationally designed polypharmacology. Nat Commun. 2017 Nov 10;8(1):1420. | ||||
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