Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T42065 | Target Info | |||
| Target Name | N-acetylmannosamine kinase (GNE) | ||||
| Synonyms | UDPGlcNAc2epimerase/ManAc kinase; GNE; Bifunctional UDPNacetylglucosamine 2epimerase/Nacetylmannosamine kinase | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | GNE | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: CMP-sialic acid | Ligand Info | |||||
| Structure Description | Crystal structure of UDP-GlcNAc 2-epimerase | PDB:4ZHT | ||||
| Method | X-ray diffraction | Resolution | 2.69 Å | Mutation | No | [1] |
| PDB Sequence |
NRKLRVCVAT
16 CNRADYSKLA26 PIFGIKTEPE37 FFELDVVVLG47 SHLIDDYGNT57 YRIEQDDFDI 68 NTRLHTIVRG78 EDEAAVESVG89 LALVKLPDVL99 NRLKPDIIVH110 GDRFDALALA 120 TSAALNIRIL131 HIEGGEVSGT141 IDDSIRHAIT151 KLAHYHVCCT161 RSAEQHLISC 172 EDHDRILLAG182 CPSYDKLLSA192 KNKDYSIIRW204 LGDDVKSKDY214 IVALQHPVTT 224 DIKHSIKFEL235 TLDALISFNK245 RTLVLFPNID255 AGSKEVRVRK267 KGIEHHPNFR 277 AVKHVPFDQF287 IQLVAHAGCI298 GNSSCGVREV308 GAFGTPVINL318 GTRQIGRETG 328 ENVLHVRDAD338 TQDKILQALH348 LQFGKQYPCS358 KIYGDGNAVP368 RILKFLKSID 378 LQEPLQKKFC388 FP
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| Ligand Name: Uridine-5'-Diphosphate | Ligand Info | |||||
| Structure Description | Crystal structure of UDP-GlcNAc 2-epimerase | PDB:4ZHT | ||||
| Method | X-ray diffraction | Resolution | 2.69 Å | Mutation | No | [1] |
| PDB Sequence |
NRKLRVCVAT
16 CNRADYSKLA26 PIFGIKTEPE37 FFELDVVVLG47 SHLIDDYGNT57 YRIEQDDFDI 68 NTRLHTIVRG78 EDEAAVESVG89 LALVKLPDVL99 NRLKPDIIVH110 GDRFDALALA 120 TSAALNIRIL131 HIEGGEVSGT141 IDDSIRHAIT151 KLAHYHVCCT161 RSAEQHLISC 172 EDHDRILLAG182 CPSYDKLLSA192 KNKDYSIIRW204 LGDDVKSKDY214 IVALQHPVTT 224 DIKHSIKFEL235 TLDALISFNK245 RTLVLFPNID255 AGSKEVRVRK267 KGIEHHPNFR 277 AVKHVPFDQF287 IQLVAHAGCI298 GNSSCGVREV308 GAFGTPVINL318 GTRQIGRETG 328 ENVLHVRDAD338 TQDKILQALH348 LQFGKQYPCS358 KIYGDGNAVP368 RILKFLKSID 378 LQEPLQKKFC388 FP
|
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ARG19
2.761
ALA20
3.600
SER23
2.811
LYS24
3.101
ARG113
3.038
LEU218
3.477
HIS220
2.495
LEU250
3.241
ASN253
2.802
LYS280
4.671
HIS281
3.312
|
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| Ligand Name: adenosine diphosphate | Ligand Info | |||||
| Structure Description | Structure of N-Acetylmannosamine kinase in complex with N- acetylmannosamine and ADP | PDB:2YHY | ||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [2] |
| PDB Sequence |
GTLSALAVDL
414 GGTNLRVAIV424 SMKGEIVKKY434 TQFNPKTYEE444 RINLILQMCV454 EAAAEAVKLN 464 CRILGVGIST474 GGRVNPREGI484 VLHSTKLIQE494 WNSVDLRTPL504 SDTLHLPVWV 514 DNDGNCAALA524 ERKFGQGKGL534 ENFVTLITGT544 GIGGGIIHQH554 ELIHGSSFCA 564 AELGHLVVSL574 DGPDCSCGSH584 GCIEAYASGM594 ALQREAKKLH604 DEDLLLVEGM 614 SAVGALHLIQ629 AAKLGNAKAQ639 SILRTAGTAL649 GLGVVNILHT659 MNPSLVILSG 669 VLASHYIHIV679 KDVIRQQALS689 SVQDVDVVVS699 DLVDPALLGA709 ASMVLDYT |
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .A:413 or .A:415 or .A:416 or .A:417 or .A:418 or .A:420 or .A:542 or .A:543 or .A:544 or .A:545 or .A:593 or .A:594 or .A:597 or .A:623 or .A:624 or .A:625 or .A:670 or .A:671; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Selenomethionine | Ligand Info | |||||
| Structure Description | Crystal structure of UDP-GlcNAc 2-epimerase | PDB:4ZHT | ||||
| Method | X-ray diffraction | Resolution | 2.69 Å | Mutation | No | [1] |
| PDB Sequence |
NRKLRVCVAT
16 CNRADYSKLA26 PIFGIKTEPE37 FFELDVVVLG47 SHLIDDYGNT57 YRIEQDDFDI 68 NTRLHTIVRG78 EDEAAVESVG89 LALVKLPDVL99 NRLKPDIIVH110 GDRFDALALA 120 TSAALNIRIL131 HIEGGEVSGT141 IDDSIRHAIT151 KLAHYHVCCT161 RSAEQHLISC 172 EDHDRILLAG182 CPSYDKLLSA192 KNKDYSIIRW204 LGDDVKSKDY214 IVALQHPVTT 224 DIKHSIKFEL235 TLDALISFNK245 RTLVLFPNID255 AGSKEVRVRK267 KGIEHHPNFR 277 AVKHVPFDQF287 IQLVAHAGCI298 GNSSCGVREV308 GAFGTPVINL318 GTRQIGRETG 328 ENVLHVRDAD338 TQDKILQALH348 LQFGKQYPCS358 KIYGDGNAVP368 RILKFLKSID 378 LQEPLQKKFC388 FP
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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 .MSE or .MSE2 or .MSE3 or :3MSE;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:22 or .A:25 or .A:26 or .A:27 or .A:28 or .A:30 or .A:31 or .A:32 or .A:33 or .A:34 or .A:41 or .A:43 or .A:56 or .A:57 or .A:58 or .A:59 or .A:61 or .A:62 or .A:63 or .A:64 or .A:66 or .A:80 or .A:81 or .A:82 or .A:83 or .A:85 or .A:86 or .A:87 or .A:88 or .A:95 or .A:96 or .A:99 or .A:100 or .A:105 or .A:106 or .A:108 or .A:109 or .A:114 or .A:119 or .A:120 or .A:121 or .A:122 or .A:123 or .A:124 or .A:125 or .A:127 or .A:128 or .A:129 or .A:130 or .A:131 or .A:135 or .A:136 or .A:148 or .A:151 or .A:152 or .A:166 or .A:167 or .A:168 or .A:169 or .A:170 or .A:172 or .A:173 or .A:196 or .A:197 or .A:199 or .A:200 or .A:201 or .A:202 or .A:204 or .A:205 or .A:206 or .A:209 or .A:210 or .A:211 or .A:215 or .A:216 or .A:218 or .A:219 or .A:220 or .A:221 or .A:223 or .A:228 or .A:229 or .A:230 or .A:231 or .A:233 or .A:234 or .A:235 or .A:236 or .A:237 or .A:249 or .A:250 or .A:251 or .A:252 or .A:254 or .A:255 or .A:256 or .A:257 or .A:258 or .A:259 or .A:260 or .A:262 or .A:263 or .A:264 or .A:266 or .A:267 or .A:268 or .A:269 or .A:270 or .A:271 or .A:281 or .A:283 or .A:286 or .A:287 or .A:291 or .A:294 or .A:295 or .A:296 or .A:298 or .A:299 or .A:301 or .A:303 or .A:304 or .A:308 or .A:313 or .A:314 or .A:315 or .A:316 or .A:318 or .A:319 or .A:335 or .A:337 or .A:343; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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CYS13
3.221
VAL14
3.826
ALA15
4.891
THR16
4.314
TYR22
3.526
LEU25
2.962
ALA26
3.081
PRO27
3.373
ILE28
1.323
PHE30
1.331
GLY31
3.275
ILE32
3.411
LYS33
2.975
THR34
4.951
LEU41
4.210
VAL43
4.477
ASN56
4.725
THR57
3.056
TYR58
3.205
ARG59
1.338
ILE61
1.319
GLU62
3.429
GLN63
3.611
ASP64
3.225
PHE66
3.550
ASP80
2.971
GLU81
3.197
ALA82
3.343
ALA83
1.316
VAL85
1.332
GLU86
3.386
SER87
3.316
VAL88
3.235
LEU95
4.902
PRO96
3.714
LEU99
3.410
ASN100
4.874
ASP105
4.595
ILE106
1.326
ILE108
1.328
VAL109
3.711
PHE114
3.579
LEU119
3.155
ALA120
4.510
THR121
4.853
SER122
2.945
ALA123
3.222
ALA124
3.234
LEU125
1.330
ASN127
1.340
ILE128
3.231
ARG129
2.768
ILE130
3.347
LEU131
2.939
GLY135
4.796
GLY136
4.749
HIS148
3.283
THR151
4.579
LYS152
2.830
GLN166
4.810
HIS167
2.792
LEU168
3.210
ILE169
3.218
SER170
1.322
CYS172
1.342
GLU173
3.423
ASP196
3.235
TYR197
1.331
SER199
1.330
ILE200
3.201
ILE201
3.218
ARG202
1.324
TRP204
1.341
LEU205
3.657
GLY206
4.807
VAL209
4.194
LYS210
4.499
SER211
4.030
ILE215
4.929
VAL216
3.335
LEU218
3.944
GLN219
3.633
HIS220
3.899
PRO221
3.796
THR223
4.356
HIS228
2.909
SER229
3.632
ILE230
3.269
LYS231
1.325
PHE233
1.325
GLU234
3.363
LEU235
3.315
THR236
2.634
LEU237
4.122
VAL249
4.012
LEU250
4.417
PHE251
3.621
PRO252
3.455
ILE254
4.217
ASP255
4.058
ALA256
3.696
GLY257
3.224
SER258
3.267
LYS259
3.300
GLU260
1.329
VAL262
1.337
ARG263
3.181
VAL264
1.322
ARG266
1.338
LYS267
3.354
LYS268
3.287
GLY269
3.314
ILE270
3.233
GLU271
4.338
HIS281
3.730
PRO283
4.131
GLN286
3.386
PHE287
4.458
VAL291
3.898
ALA294
4.929
GLY295
4.714
CYS296
1.322
ILE298
1.324
GLY299
4.551
SER301
3.888
CYS303
3.937
GLY304
4.160
VAL308
3.738
THR313
4.518
PRO314
2.982
VAL315
3.374
ILE316
2.824
LEU318
4.075
GLY319
3.801
ARG335
3.854
ALA337
3.698
ILE343
4.384
|
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| Ligand Name: (3S)-3-Aminopyrrolidine-2,5-dione | Ligand Info | |||||
| Structure Description | High-resolution crystal structures of N-Acetylmannosamine kinase: Insights about substrate specificity, activity and inhibitor modelling. | PDB:2YHW | ||||
| Method | X-ray diffraction | Resolution | 1.64 Å | Mutation | No | [2] |
| PDB Sequence |
GTLSALAVDL
414 GGTNLRVAIV424 SMKGEIVKKY434 TQFNPKTYEE444 RINLILQMCV454 EAAAEAVKLN 464 CRILGVGIST474 GGRVNPREGI484 VLHSTKLIQE494 WNSVDLRTPL504 SDTLHLPVWV 514 DNDGNCAALA524 ERKFGQGKGL534 ENFVTLITGT544 GIGGGIIHQH554 ELIHGSSFCA 564 AELGHLVVSL574 GPDCSCGSHG585 CIEAYASGMA595 LQREAKKLHD605 EDLLLVEGMS 615 VAVGALHLIQ629 AAKLGNAKAQ639 SILRTAGTAL649 GLGVVNILHT659 MNPSLVILSG 669 VLASHYIHIV679 KDVIRQQALS689 SVQDVDVVVS699 DLVDPALLGA709 ASMVLDYT |
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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 .SNN or .SNN2 or .SNN3 or :3SNN;style chemicals stick;color identity;select .A:573 or .A:574 or .A:576 or .A:577 or .A:584 or .A:585 or .A:590; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-(Acetylamino)-2-deoxy-alpha-D-mannopyranose | Ligand Info | |||||
| Structure Description | High-resolution crystal structures of N-Acetylmannosamine kinase: Insights about substrate specificity, activity and inhibitor modelling. | PDB:2YHW | ||||
| Method | X-ray diffraction | Resolution | 1.64 Å | Mutation | No | [2] |
| PDB Sequence |
GTLSALAVDL
414 GGTNLRVAIV424 SMKGEIVKKY434 TQFNPKTYEE444 RINLILQMCV454 EAAAEAVKLN 464 CRILGVGIST474 GGRVNPREGI484 VLHSTKLIQE494 WNSVDLRTPL504 SDTLHLPVWV 514 DNDGNCAALA524 ERKFGQGKGL534 ENFVTLITGT544 GIGGGIIHQH554 ELIHGSSFCA 564 AELGHLVVSL574 GPDCSCGSHG585 CIEAYASGMA595 LQREAKKLHD605 EDLLLVEGMS 615 VAVGALHLIQ629 AAKLGNAKAQ639 SILRTAGTAL649 GLGVVNILHT659 MNPSLVILSG 669 VLASHYIHIV679 KDVIRQQALS689 SVQDVDVVVS699 DLVDPALLGA709 ASMVLDYT |
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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 .BM3 or .BM32 or .BM33 or :3BM3;style chemicals stick;color identity;select .A:475 or .A:476 or .A:477 or .A:487 or .A:488 or .A:489 or .A:491 or .A:492 or .A:516 or .A:517 or .A:518 or .A:545 or .A:546 or .A:547 or .A:548 or .A:566 or .A:569 or .A:588; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-(acetylamino)-2-deoxy-6-O-phosphono-alpha-D-mannopyranose | Ligand Info | |||||
| Structure Description | Crystal structure of N-Acetylmannosamine kinase in complex with N- acetyl mannosamine 6-phosphate and ADP. | PDB:2YI1 | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [2] |
| PDB Sequence |
GTLSALAVDL
414 GGTNLRVAIV424 SMKGEIVKKY434 TQFNPKTYEE444 RINLILQMCV454 EAAAEAVKLN 464 CRILGVGIST474 GGRVNPREGI484 VLHSTKLIQE494 WNSVDLRTPL504 SDTLHLPVWV 514 DNDGNCAALA524 ERKFGQGKGL534 ENFVTLITGT544 GIGGGIIHQH554 ELIHGSSFCA 564 AELGHLVVSL574 DGPDCSCGSH584 GCIEAYASGM594 ALQREAKKLH604 DEDLLLVEGM 614 SAVGALHLIQ629 AAKLGNAKAQ639 SILRTAGTAL649 GLGVVNILHT659 MNPSLVILSG 669 VLASHYIHIV679 KDVIRQQALS689 SVQDVDVVVS699 DLVDPALLGA709 ASMVLDYT |
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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 .BMX or .BMX2 or .BMX3 or :3BMX;style chemicals stick;color identity;select .A:415 or .A:416 or .A:417 or .A:475 or .A:476 or .A:477 or .A:487 or .A:488 or .A:489 or .A:491 or .A:492 or .A:516 or .A:517 or .A:518 or .A:542 or .A:543 or .A:544 or .A:545 or .A:546 or .A:547 or .A:548 or .A:566 or .A:569 or .A:588; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLY415
3.680
GLY416
2.697
THR417
4.740
GLY475
3.613
GLY476
3.011
ARG477
2.968
HIS487
4.637
SER488
3.639
THR489
2.855
LEU491
3.679
ILE492
3.854
ASN516
3.197
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Mechanism and inhibition of human UDP-GlcNAc 2-epimerase, the key enzyme in sialic acid biosynthesis. Sci Rep. 2016 Mar 16;6:23274. | ||||
| REF 2 | Crystal structures of N-acetylmannosamine kinase provide insights into enzyme activity and inhibition. J Biol Chem. 2012 Apr 20;287(17):13656-65. | ||||
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