Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T89360 | Target Info | |||
| Target Name | Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2) | ||||
| Synonyms | IMPDH-II; IMPDH 2; IMPD2; IMPD 2; IMP dehydrogenase 2 | ||||
| Target Type | Successful Target | ||||
| Gene Name | IMPDH2 | ||||
| Biochemical Class | CH-OH donor oxidoreductase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Nicotinamide-Adenine-Dinucleotide | Ligand Info | |||
| Canonical SMILES | C1=CC(=C[N+](=C1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)N4C=NC5=C(N=CN=C54)N)O)O)O)O)C(=O)N | ||||
| InChI | 1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 | ||||
| InChIKey | BAWFJGJZGIEFAR-NNYOXOHSSA-N | ||||
| PubChem Compound ID | 5892 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1NFB Ternary complex of the human type II Inosine Monophosphate Dedhydrogenase with 6Cl-IMP and NAD | ||||||
| Method | X-ray diffraction | Resolution | 2.90 Å | Mutation | No | [1] |
| PDB Sequence |
TSYVPDDGLT
19 AQQLFNCGDG29 LTYNDFLILP39 GYIDFTADQV49 DLTSALTKKI59 TLKTPLVSSP 69 MDTVTEAGMA79 IAMALTGGIG89 FIHHNCTPEF99 QANEVRKVKK109 YEQGFITDPV 119 VLSPGIPITD146 TGRMGSAPAG191 ITLKEANEIL201 QRSKKGKLPI211 VNEDDEVAII 222 ANRDYPLASK238 DAKKQLLCGA248 AIGTHEDDKY258 RLDLLAQAGV268 DVVVLDSSQG 278 NSIFQINMIK288 YIKDKYPNLQ298 VIGGNVVTAA308 QAKNLIDAGV318 DALRVGMGSG 328 SICITQEVLA338 CGRPQATAVY348 KVSEYARRFG358 VPVIADGGIQ368 NVGHIAKALA 378 LGASTVMMGS388 LLAATTEAPG398 EYFFSDGIRL408 KKYRGMDKGS452 IHKFVPYLIA 462 GIQHSCQDIG472 AKSLTQVRAM482 MYSGELKFEK492 RTSSAQ
|
|||||
|
|
||||||
| PDB ID: 6U8S Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Filament assembly interface reconstruction. | ||||||
| Method | Electron microscopy | Resolution | 3.14 Å | Mutation | No | [2] |
| PDB Sequence |
MADYLISGGT
10 SYVPDDGLTA20 QQLFNCGDGL30 TYNDFLILPG40 YIDFTADQVD50 LTSALTKKIT 60 LKTPLVSSPM70 DTVTEAGMAI80 AMALTGGIGF90 IHHNCTPEFQ100 ANEVRKVKKY 110 YPLASKDAKK242 QLLCGAAIGT252 HEDDKYRLDL262 LAQAGVDVVV272 LDSSQGNSIF 282 QINMIKYIKD292 KYPNLQVIGG302 NVVTAAQAKN312 LIDAGVDALR322 VGMGSGSICI 332 TQEVLACGRP342 QATAVYKVSE352 YARRFGVPVI362 ADGGIQNVGH372 IAKALALGAS 382 TVMMGSLLAA392 TTEAPGEYFF402 SDGIRLKKYR412 GMGSLDAMIK438 VAQGVSGAVQ 448 DKGSIHKFVP458 YLIAGIQHSC468 QDIGAKSLTQ478 VRAMMYSGEL488 KFEKRTSSAQ 498 VEGGVHSLHS508 YEKRLF
|
|||||
|
|
HIS93
3.546
THR252
3.485
HIS253
3.170
GLU254
3.928
ASP274
2.636
SER275
3.377
SER276
2.991
GLN277
4.884
PHE282
3.344
ASN303
2.864
GLY324
3.487
|
|||||
| PDB ID: 6U8E Human IMPDH2 treated with ATP, IMP, and NAD+. Filament assembly interface reconstruction. | ||||||
| Method | Electron microscopy | Resolution | 3.03 Å | Mutation | No | [2] |
| PDB Sequence |
MADYLISGGT
10 SYVPDDGLTA20 QQLFNCGDGL30 TYNDFLILPG40 YIDFTADQVD50 LTSALTKKIT 60 LKTPLVSSPM70 DTVTEAGMAI80 AMALTGGIGF90 IHHNCTPEFQ100 ANEVRKVKKY 110 PLASKDAKKQ243 LLCGAAIGTH253 EDDKYRLDLL263 AQAGVDVVVL273 DSSQGNSIFQ 283 INMIKYIKDK293 YPNLQVIGGN303 VVTAAQAKNL313 IDAGVDALRV323 GMGSGSICIT 333 QEVLACGRPQ343 ATAVYKVSEY353 ARRFGVPVIA363 DGGIQNVGHI373 AKALALGAST 383 VMMGSLLAAT393 TEAPGEYFFS403 DGIRLKKYRG413 MGSLDAMIKV439 AQGVSGAVQD 449 KGSIHKFVPY459 LIAGIQHSCQ469 DIGAKSLTQV479 RAMMYSGELK489 FEKRTSSAQV 499 EGGVHSLHSY509 EKRLF
|
|||||
|
|
HIS93
3.866
THR252
4.044
HIS253
3.153
GLU254
4.404
ASP274
2.660
SER275
3.470
SER276
2.831
GLN277
4.423
PHE282
3.237
ASN303
2.366
|
|||||
| PDB ID: 6U9O Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Fully compressed filament segment reconstruction. | ||||||
| Method | Electron microscopy | Resolution | 3.36 Å | Mutation | No | [2] |
| PDB Sequence |
SYVPDDGLTA
20 QQLFNCGDGL30 TYNDFLILPG40 YIDFTADQVD50 LTSALTKKIT60 LKTPLVSSPM 70 DTVTEAGMAI80 AMALTGGIGF90 IHHNCTPEFQ100 ANEVRKVKKY110 EQGFITDPVV 120 LSPKDRVRDV130 FEAKARHGFC140 GIPITDTGRM150 GSRLVGIISS160 RDIDFLKEEE 170 HDCFLEEIMT180 KREDLVVAPA190 GITLKEANEI200 LQRSKKGKLP210 IVNEDDELVA 220 IIARTDLKKN230 RDYPLASKDA240 KKQLLCGAAI250 GTHEDDKYRL260 DLLAQAGVDV 270 VVLDSSQGNS280 IFQINMIKYI290 KDKYPNLQVI300 GGNVVTAAQA310 KNLIDAGVDA 320 LRVGMGSGSI330 CITQEVLACG340 RPQATAVYKV350 SEYARRFGVP360 VIADGGIQNV 370 GHIAKALALG380 ASTVMMGSLL390 AATTEAPGEY400 FFSDGIRLKK410 YRGMGSLDAM 420 IKVAQGVSGA446 VQDKGSIHKF456 VPYLIAGIQH466 SCQDIGAKSL476 TQVRAMMYSG 486 ELKFEKRTSS496 AQVEGGVHSL506 HSYEKRLF
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NAD or .NAD2 or .NAD3 or :3NAD;style chemicals stick;color identity;select .A:93 or .A:252 or .A:253 or .A:254 or .A:274 or .A:275 or .A:276 or .A:282 or .A:303 or .A:324 or .A:325 or .A:326 or .A:331 or .A:333 or .A:364 or .A:414 or .A:415 or .A:441; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 6UA4 Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Bent (3/4 compressed, 1/4 extended) segment reconstruction. | ||||||
| Method | Electron microscopy | Resolution | 3.65 Å | Mutation | No | [2] |
| PDB Sequence |
SYVPDDGLTA
20 QQLFNCGDGL30 TYNDFLILPG40 YIDFTADQVD50 LTSALTKKIT60 LKTPLVSSPM 70 DTVTEAGMAI80 AMALTGGIGF90 IHHNCTPEFQ100 ANEVRKVKKY110 EQGFITDPVV 120 LSPKDRVRDV130 FEAKARHGFC140 GIPITDTGRM150 GSRLVGIISS160 RDIDFLKEEE 170 HDCFLEEIMT180 KREDLVVAPA190 GITLKEANEI200 LQRSKKGKLP210 IVNEDDELVA 220 IIARTDLKKN230 RDYPLASKDA240 KKQLLCGAAI250 GTHEDDKYRL260 DLLAQAGVDV 270 VVLDSSQGNS280 IFQINMIKYI290 KDKYPNLQVI300 GGNVVTAAQA310 KNLIDAGVDA 320 LRVGMGSGSI330 CITQEVLACG340 RPQATAVYKV350 SEYARRFGVP360 VIADGGIQNV 370 GHIAKALALG380 ASTVMMGSLL390 AATTEAPGEY400 FFSDGIRLKK410 YRGMGSLDAM 420 IKVAQGVSGA446 VQDKGSIHKF456 VPYLIAGIQH466 SCQDIGAKSL476 TQVRAMMYSG 486 ELKFEKRTSS496 AQVEGGVHSL506 HSYEKRLF
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NAD or .NAD2 or .NAD3 or :3NAD;style chemicals stick;color identity;select .A:93 or .A:252 or .A:253 or .A:254 or .A:274 or .A:275 or .A:276 or .A:277 or .A:280 or .A:282 or .A:303 or .A:322 or .A:324 or .A:325 or .A:326 or .A:327 or .A:328 or .A:331 or .A:333 or .A:364 or .A:414 or .A:415 or .A:441; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS93
4.239
THR252
3.741
HIS253
3.413
GLU254
3.635
ASP274
2.449
SER275
2.837
SER276
2.544
GLN277
4.439
SER280
4.443
PHE282
3.362
ASN303
2.553
ARG322
4.245
|
|||||
| PDB ID: 6UA5 Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Free interfacial octamer reconstruction. | ||||||
| Method | Electron microscopy | Resolution | 3.79 Å | Mutation | No | [2] |
| PDB Sequence |
MADYLISGGT
10 SYVPDDGLTA20 QQLFNCGDGL30 TYNDFLILPG40 YIDFTADQVD50 LTSALTKKIT 60 LKTPLVSSPM70 DTVTEAGMAI80 AMALTGGIGF90 IHHNCTPEFQ100 ANEVRKVKKY 110 YPLASKDAKK242 QLLCGAAIGT252 HEDDKYRLDL262 LAQAGVDVVV272 LDSSQGNSIF 282 QINMIKYIKD292 KYPNLQVIGG302 NVVTAAQAKN312 LIDAGVDALR322 VGMGSGSICI 332 TQEVLACGRP342 QATAVYKVSE352 YARRFGVPVI362 ADGGIQNVGH372 IAKALALGAS 382 TVMMGSLLAA392 TTEAPGEYFF402 SDGIRLKKYR412 GMGSLDAMIK438 VAQGVSGAVQ 448 DKGSIHKFVP458 YLIAGIQHSC468 QDIGAKSLTQ478 VRAMMYSGEL488 KFEKRTSSAQ 498 VEGGVHSLHS508 YEKRLF
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NAD or .NAD2 or .NAD3 or :3NAD;style chemicals stick;color identity;select .A:93 or .A:252 or .A:253 or .A:254 or .A:274 or .A:275 or .A:276 or .A:277 or .A:282 or .A:303 or .A:322 or .A:324 or .A:325 or .A:326 or .A:331 or .A:333 or .A:364 or .A:414 or .A:415 or .A:441; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS93
3.564
THR252
3.439
HIS253
3.355
GLU254
4.299
ASP274
2.552
SER275
3.941
SER276
3.106
GLN277
4.977
PHE282
3.273
ASN303
2.821
|
|||||
| PDB ID: 6UAJ Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Free canonical octamer reconstruction. | ||||||
| Method | Electron microscopy | Resolution | 3.84 Å | Mutation | No | [2] |
| PDB Sequence |
TSYVPDDGLT
19 AQQLFNCGDG29 LTYNDFLILP39 GYIDFTADQV49 DLTSALTKKI59 TLKTPLVSSP 69 MDTVTEAGMA79 IAMALTGGIG89 FIHHNCTPEF99 QANEVRKVKK109 YEQGFITDPV 119 VLSPKDRVRD129 VFEAKARHGF139 CGIPITDTGR149 MGSRLVGIIS159 SRDIDFLKEE 169 EHDCFLEEIM179 TKREDLVVAP189 AGITLKEANE199 ILQRSKKGKL209 PIVNEDDELV 219 AIIARTDLKK229 NRDYPLASKD239 AKKQLLCGAA249 IGTHEDDKYR259 LDLLAQAGVD 269 VVVLDSSQGN279 SIFQINMIKY289 IKDKYPNLQV299 IGGNVVTAAQ309 AKNLIDAGVD 319 ALRVGMGSGS329 ICITQEVLAC339 GRPQATAVYK349 VSEYARRFGV359 PVIADGGIQN 369 VGHIAKALAL379 GASTVMMGSL389 LAATTEAPGE399 YFFSDGIRLK409 KYRGMGSLDA 419 MIKVAQGVSG445 AVQDKGSIHK455 FVPYLIAGIQ465 HSCQDIGAKS475 LTQVRAMMYS 485 GELKFEKRTS495 SAQVEGGVHS505 LHSYEKRLF
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NAD or .NAD2 or .NAD3 or :3NAD;style chemicals stick;color identity;select .A:93 or .A:252 or .A:253 or .A:254 or .A:274 or .A:275 or .A:276 or .A:277 or .A:282 or .A:303 or .A:322 or .A:324 or .A:325 or .A:331 or .A:333 or .A:364 or .A:414 or .A:415 or .A:441; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 6U8R Human IMPDH2 treated with ATP, IMP, and NAD+. Bent (1/4 compressed, 3/4 extended) segment reconstruction. | ||||||
| Method | Electron microscopy | Resolution | 3.91 Å | Mutation | No | [2] |
| PDB Sequence |
SYVPDDGLTA
20 QQLFNCGDGL30 TYNDFLILPG40 YIDFTADQVD50 LTSALTKKIT60 LKTPLVSSPM 70 DTVTEAGMAI80 AMALTGGIGF90 IHHNCTPEFQ100 ANEVRKVKKY110 EQGFITDPVV 120 LSPKDRVRDV130 FEAKARHGFC140 GIPITDTGRM150 GSRLVGIISS160 RDIDFLKEEE 170 HDCFLEEIMT180 KREDLVVAPA190 GITLKEANEI200 LQRSKKGKLP210 IVNEDDELVA 220 IIARTDLKKN230 RDYPLASKDA240 KKQLLCGAAI250 GTHEDDKYRL260 DLLAQAGVDV 270 VVLDSSQGNS280 IFQINMIKYI290 KDKYPNLQVI300 GGNVVTAAQA310 KNLIDAGVDA 320 LRVGMGSGSI330 CITQEVLACG340 RPQATAVYKV350 SEYARRFGVP360 VIADGGIQNV 370 GHIAKALALG380 ASTVMMGSLL390 AATTEAPGEY400 FFSDGIRLKK410 YRGMGSLDAM 420 IKVAQGVSGA446 VQDKGSIHKF456 VPYLIAGIQH466 SCQDIGAKSL476 TQVRAMMYSG 486 ELKFEKRTSS496 AQVEGGVHSL506 HSYEKRLF
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NAD or .NAD2 or .NAD3 or :3NAD;style chemicals stick;color identity;select .A:93 or .A:252 or .A:253 or .A:254 or .A:274 or .A:275 or .A:276 or .A:282 or .A:303 or .A:324 or .A:325 or .A:326 or .A:327 or .A:328 or .A:331 or .A:333 or .A:414 or .A:415 or .A:441; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 6UA2 Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Bent (2/4 compressed, 2/4 extended) segment reconstruction. | ||||||
| Method | Electron microscopy | Resolution | 4.20 Å | Mutation | No | [2] |
| PDB Sequence |
SYVPDDGLTA
20 QQLFNCGDGL30 TYNDFLILPG40 YIDFTADQVD50 LTSALTKKIT60 LKTPLVSSPM 70 DTVTEAGMAI80 AMALTGGIGF90 IHHNCTPEFQ100 ANEVRKVKKY110 EQGFITDPVV 120 LSPKDRVRDV130 FEAKARHGFC140 GIPITDTGRM150 GSRLVGIISS160 RDIDFLKEEE 170 HDCFLEEIMT180 KREDLVVAPA190 GITLKEANEI200 LQRSKKGKLP210 IVNEDDELVA 220 IIARTDLKKN230 RDYPLASKDA240 KKQLLCGAAI250 GTHEDDKYRL260 DLLAQAGVDV 270 VVLDSSQGNS280 IFQINMIKYI290 KDKYPNLQVI300 GGNVVTAAQA310 KNLIDAGVDA 320 LRVGMGSGSI330 CITQEVLACG340 RPQATAVYKV350 SEYARRFGVP360 VIADGGIQNV 370 GHIAKALALG380 ASTVMMGSLL390 AATTEAPGEY400 FFSDGIRLKK410 YRGMGSLDAM 420 IKVAQGVSGA446 VQDKGSIHKF456 VPYLIAGIQH466 SCQDIGAKSL476 TQVRAMMYSG 486 ELKFEKRTSS496 AQVEGGVHSL506 HSYEKRLF
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NAD or .NAD2 or .NAD3 or :3NAD;style chemicals stick;color identity;select .A:93 or .A:251 or .A:252 or .A:253 or .A:254 or .A:274 or .A:275 or .A:276 or .A:277 or .A:282 or .A:283 or .A:303 or .A:322 or .A:324 or .A:325 or .A:326 or .A:364 or .A:414 or .A:415 or .A:441; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS93
4.610
GLY251
4.901
THR252
2.344
HIS253
3.327
GLU254
4.526
ASP274
2.832
SER275
2.804
SER276
2.491
GLN277
4.807
PHE282
3.135
|
|||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The Conformation of NAD Bound to Human Inosine Monophosphate Dehydrogenase Type II | ||||
| REF 2 | Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. Elife. 2020 Jan 30;9:e53243. | ||||
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