Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T86573 | Target Info | |||
| Target Name | HUMAN inosine-5'-monophosphate dehydrogenase 2 (IMPDH2) | ||||
| Synonyms | IMPDH-II; IMPDH 2; IMPD2; IMPD 2; IMP dehydrogenase 2 | ||||
| Gene Name | IMPDH2 | ||||
| Biochemical Class | CH-OH donor oxidoreductase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Guanosine-5'-Triphosphate | Ligand Info | |||
| Canonical SMILES | C1=NC2=C(N1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N | ||||
| InChI | 1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 | ||||
| InChIKey | XKMLYUALXHKNFT-UUOKFMHZSA-N | ||||
| PubChem Compound ID | 135398633 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6I0O Structure of human IMP dehydrogenase, isoform 2, bound to GTP | ||||||
| Method | X-ray diffraction | Resolution | 2.62 Å | Mutation | No | [1] |
| 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 LRVGMEVLAC339 GRPQATAVYK349 VSEYARRFGV359 PVIADGGIQN369 VGHIAKALAL 379 GASTVMMGSL389 LAATTEAPGE399 YFFSKGSIHK455 FVPYLIAGIQ465 HSCQDIGAKS 475 LTQVRAMMYS485 GELKFEKRTS495 SAQV
|
|||||
|
|
LYS62
3.301
LYS109
2.515
TYR110
2.871
GLU111
2.492
GLN112
2.152
GLY113
2.417
PHE114
4.834
ILE115
2.695
ASP117
4.479
PRO118
2.494
VAL119
2.638
LYS134
3.398
GLY138
3.914
PHE139
2.549
CYS140
2.125
GLY141
1.583
ILE142
3.585
PRO143
4.107
ILE157
2.242
ILE158
3.235
SER159
1.842
SER160
1.606
ARG161
2.424
ASP162
2.319
MET179
4.979
THR180
2.461
ASP184
2.620
LEU185
2.488
VAL186
1.843
LEU194
2.622
LYS195
3.764
ASN198
1.962
GLN202
4.486
LYS205
4.572
LYS206
2.699
GLY207
1.740
LYS208
2.007
LEU209
3.904
PRO210
3.456
ILE221
3.620
ILE222
3.374
ALA223
3.603
THR225
2.173
ASP226
1.908
LEU227
3.072
LYS229
1.710
ASN230
1.675
TYR233
3.054
PRO234
2.756
LEU235
4.212
ALA236
3.653
LYS238
1.785
LYS242
2.196
|
|||||
| PDB ID: 6UDO Human IMPDH2 treated with ATP, IMP, and 20 mM GTP. Fully compressed filament segment reconstruction. | ||||||
| Method | Electron microscopy | Resolution | 3.21 Å | Mutation | No | [2] |
| PDB Sequence |
YVPDDGLTAQ
21 QLFNCGDGLT31 YNDFLILPGY41 IDFTADQVDL51 TSALTKKITL61 KTPLVSSPMD 71 TVTEAGMAIA81 MALTGGIGFI91 HHNCTPEFQA101 NEVRKVKKYE111 QGFITDPVVL 121 SPKDRVRDVF131 EAKARHGFCG141 IPITDTGRMG151 SRLVGIISSR161 DIDFLKEEEH 171 DCFLEEIMTK181 REDLVVAPAG191 ITLKEANEIL201 QRSKKGKLPI211 VNEDDELVAI 221 IARTDLKKNR231 DYPLASKDAK241 KQLLCGAAIG251 THEDDKYRLD261 LLAQAGVDVV 271 VLDSSQGNSI281 FQINMIKYIK291 DKYPNLQVIG301 GNVVTAAQAK311 NLIDAGVDAL 321 RVGMGSGSIC331 ITQEVLACGR341 PQATAVYKVS351 EYARRFGVPV361 IADGGIQNVG 371 HIAKALALGA381 STVMMGSLLA391 ATTEAPGEYF401 FSDGIRLKKY411 RGMGSLDAMI 437 KVAQGVSGAV447 QDKGSIHKFV457 PYLIAGIQHS467 CQDIGAKSLT477 QVRAMMYSGE 487 LKFEKRTSSA497 QVEGGVHSLH507 SYEKRLF
|
|||||
|
|
LYS109
3.212
TYR110
4.081
GLU111
3.863
GLN112
3.595
GLY113
4.106
ILE115
3.644
ASP117
4.423
PRO118
3.631
VAL119
4.359
LYS134
4.646
GLY138
4.417
PHE139
3.338
CYS140
2.876
GLY141
2.661
SER159
2.567
|
|||||
| 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
|
|||||
|
|
LYS109
4.036
TYR110
4.058
GLU111
2.929
GLN112
3.832
GLY113
3.976
ILE115
3.744
PRO118
3.304
VAL119
3.567
LYS134
4.475
GLY138
4.609
PHE139
3.347
CYS140
2.609
GLY141
2.873
PRO143
4.926
SER159
4.687
SER160
3.350
|
|||||
| 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
|
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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 .GTP or .GTP2 or .GTP3 or :3GTP;style chemicals stick;color identity;select .A:109 or .A:110 or .A:111 or .A:112 or .A:113 or .A:115 or .A:117 or .A:118 or .A:119 or .A:138 or .A:139 or .A:140 or .A:141 or .A:143 or .A:159 or .A:160 or .A:194 or .A:195 or .A:198 or .A:208 or .A:221 or .A:222 or .A:223 or .A:225 or .A:226 or .A:227 or .A:229 or .A:230 or .A:242; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LYS109
3.228
TYR110
4.324
GLU111
4.370
GLN112
3.510
GLY113
4.297
ILE115
3.890
ASP117
3.902
PRO118
3.339
VAL119
3.936
GLY138
3.887
PHE139
3.254
CYS140
2.690
GLY141
3.006
PRO143
4.795
SER159
3.361
|
|||||
| 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 .GTP or .GTP2 or .GTP3 or :3GTP;style chemicals stick;color identity;select .A:109 or .A:110 or .A:111 or .A:112 or .A:115 or .A:118 or .A:119 or .A:138 or .A:139 or .A:140 or .A:141 or .A:142 or .A:159 or .A:160 or .A:161 or .A:194 or .A:195 or .A:198 or .A:208 or .A:223 or .A:225 or .A:226 or .A:227 or .A:229 or .A:230 or .A:234 or .A:238 or .A:242; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LYS109
4.139
TYR110
3.349
GLU111
3.789
GLN112
3.049
ILE115
3.305
PRO118
3.261
VAL119
3.789
GLY138
4.624
PHE139
3.280
CYS140
2.947
GLY141
2.513
ILE142
4.659
SER159
4.443
SER160
2.505
|
|||||
| 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 .GTP or .GTP2 or .GTP3 or :3GTP;style chemicals stick;color identity;select .A:109 or .A:110 or .A:111 or .A:112 or .A:115 or .A:118 or .A:119 or .A:134 or .A:138 or .A:139 or .A:140 or .A:141 or .A:142 or .A:143 or .A:159 or .A:160 or .A:194 or .A:195 or .A:198 or .A:208 or .A:225 or .A:226 or .A:229 or .A:230 or .A:238 or .A:242; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LYS109
4.880
TYR110
3.121
GLU111
3.489
GLN112
2.813
ILE115
4.434
PRO118
3.556
VAL119
4.070
LYS134
3.601
GLY138
4.006
PHE139
3.270
CYS140
2.490
GLY141
2.441
ILE142
4.978
|
|||||
| PDB ID: 6UC2 Human IMPDH2 treated with ATP and 2 mM GTP. Free canonical octamer reconstruction. | ||||||
| Method | Electron microscopy | Resolution | 4.48 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 LRVGMGSTQE335 VLACGRPQAT345 AVYKVSEYAR355 RFGVPVIADG365 GIQNVGHIAK 375 ALALGASTVM385 MGSLLAATTE395 APGEYFFSDG405 IRLKKYRGAV447 QDKGSIHKFV 457 PYLIAGIQHS467 CQDIGAKSLT477 QVRAMMYSGE487 LKFEKRTSSA497 QVE |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GTP or .GTP2 or .GTP3 or :3GTP;style chemicals stick;color identity;select .A:109 or .A:110 or .A:111 or .A:112 or .A:117 or .A:118 or .A:119 or .A:134 or .A:138 or .A:139 or .A:140 or .A:141 or .A:142 or .A:159 or .A:160 or .A:194 or .A:195 or .A:198 or .A:208 or .A:223 or .A:224 or .A:225 or .A:226 or .A:227 or .A:229 or .A:230 or .A:242; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LYS109
3.284
TYR110
3.678
GLU111
4.270
GLN112
2.957
ASP117
4.864
PRO118
3.299
VAL119
3.796
LYS134
3.751
GLY138
3.823
PHE139
3.222
CYS140
2.809
GLY141
2.296
ILE142
4.358
SER159
4.517
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | A Nucleotide-Dependent Conformational Switch Controls the Polymerization of Human IMP Dehydrogenases to Modulate their Catalytic Activity. J Mol Biol. 2019 Mar 1;431(5):956-969. | ||||
| REF 2 | Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. Elife. 2020 Jan 30;9:e53243. | ||||
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