Binding Site Information of Target
Target General Information | Top | ||||
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Target ID | T78543 | Target Info | |||
Target Name | Protein kinase G1 (PRKG1) | ||||
Synonyms | cGMP-dependent protein kinase I; cGMP-dependent protein kinase 1; cGKI; cGK1; cGK 1; PRKGR1B; PRKGR1A; PRKG1B | ||||
Target Type | Literature-reported Target | ||||
Gene Name | PRKG1 | ||||
Biochemical Class | Kinase | ||||
UniProt ID |
Drug Binding Sites of Target | Top | |||||
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Ligand Name: AMP-PNP | Ligand Info | |||||
Structure Description | Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain in AMP-PNP bound state | PDB:6BG2 | ||||
Method | X-ray diffraction | Resolution | 1.83 Å | Mutation | No | [1] |
PDB Sequence |
EDAEAKAKYE
346 AEAAFFANLK356 LSDFNIIDTL366 GVGGFGRVEL376 VQLKSEESKT386 FAMKILKKRH 396 IVDTRQQEHI406 RSEKQIMQGA416 HSDFIVRLYR426 TFKDSKYLYM436 LMEACLGGEL 446 WTILRDRGSF456 EDSTTRFYTA466 CVVEAFAYLH476 SKGIIYRDLK486 PENLILDHRG 496 YAKLVDFGFA506 KKIGFGKKTW516 FCGTPEYVAP527 EIILNKGHDI537 SADYWSLGIL 547 MYELLTGSPP557 FSGPDPMKTY567 NIILRGIDMI577 EFPKKIAKNA587 ANLIKKLCRD 597 NPSERLGNLK607 NGVKDIQKHK617 WFEGFNWEGL627 RKGTLTPPII637 PSVASPTDTS 647 NFDSFPEDND657 EPPPDDNSGW667 DIDF
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LEU366
3.734
GLY367
3.535
VAL368
4.424
GLY369
3.459
GLY370
3.049
PHE371
2.894
GLY372
3.075
VAL374
3.354
ALA388
3.394
LYS390
2.811
GLU409
4.715
VAL422
3.724
MET438
3.673
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Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
Ligand Name: Phosphonothreonine | Ligand Info | |||||
Structure Description | Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain in AMP-PNP bound state | PDB:6BG2 | ||||
Method | X-ray diffraction | Resolution | 1.83 Å | Mutation | No | [1] |
PDB Sequence |
EDAEAKAKYE
346 AEAAFFANLK356 LSDFNIIDTL366 GVGGFGRVEL376 VQLKSEESKT386 FAMKILKKRH 396 IVDTRQQEHI406 RSEKQIMQGA416 HSDFIVRLYR426 TFKDSKYLYM436 LMEACLGGEL 446 WTILRDRGSF456 EDSTTRFYTA466 CVVEAFAYLH476 SKGIIYRDLK486 PENLILDHRG 496 YAKLVDFGFA506 KKIGFGKKTW516 FCGTPEYVAP527 EIILNKGHDI537 SADYWSLGIL 547 MYELLTGSPP557 FSGPDPMKTY567 NIILRGIDMI577 EFPKKIAKNA587 ANLIKKLCRD 597 NPSERLGNLK607 NGVKDIQKHK617 WFEGFNWEGL627 RKGTLTPPII637 PSVASPTDTS 647 NFDSFPEDND657 EPPPDDNSGW667 DIDF
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Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
Ligand Name: [3H]cAMP | Ligand Info | |||||
Structure Description | Neutron diffraction reveals hydrogen bonds critical for cGMP-selective activation: Insights for PKG agonist design | PDB:4QX5 | ||||
Method | X-ray diffraction | Resolution | 1.32 Å | Mutation | No | [2] |
PDB Sequence |
IKHTEYMEFL
231 KSVPTFQSLP241 EEILSKLADV251 LEETHYENGE261 YIIRQGARGD271 TFFIISKGTV 281 NVTREDEDPV294 FLRTLGKGDW304 FGEKALQGED314 VRTANVIAAE324 AVTCLVIDRD 334 SFKHLIGGLD344 DVSNKAY
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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 .CMP or .CMP2 or .CMP3 or :3CMP;style chemicals stick;color identity;select .A:264 or .A:283 or .A:285 or .A:296 or .A:297 or .A:299 or .A:304 or .A:305 or .A:306 or .A:307 or .A:308 or .A:309 or .A:310 or .A:315 or .A:316 or .A:317 or .A:318 or .A:320 or .A:351; 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: Cyclic Guanosine Monophosphate | Ligand Info | |||||
Structure Description | Structures of PKGI Reveal a cGMP-Selective Activation Mechanism | PDB:4KU7 | ||||
Method | X-ray diffraction | Resolution | 1.65 Å | Mutation | No | [3] |
PDB Sequence |
KHTEYMEFLK
232 SVPTFQSLPE242 EILSKLADVL252 EETHYENGEY262 IIRQGARGDT272 FFIISKGTVN 282 VTREDPVFLR297 TLGKGDWFGE307 KALQGEDVRT317 ANVIAAEAVT327 CLVIDRDSFK 337 HLIGGLDDVS347 NKAY
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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 .PCG or .PCG2 or .PCG3 or :3PCG;style chemicals stick;color identity;select .A:264 or .A:283 or .A:285 or .A:296 or .A:297 or .A:299 or .A:304 or .A:305 or .A:306 or .A:307 or .A:308 or .A:309 or .A:315 or .A:316 or .A:317 or .A:318 or .A:320 or .A:351; 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: N-((3R,4R)-4-(4-(2-Fluoro-3-methoxy-6-propoxybenzoyl)benzamido)pyrrolidin-3-yl)-1H-indazole-5-carboxamide | Ligand Info | |||||
Structure Description | Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain bound with N46 | PDB:6C0T | ||||
Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [4] |
PDB Sequence |
EDAEAKAKYE
346 AEAAFFANLK356 LSDFNIIDTL366 GVGGFGRVEL376 VQLKSEESKT386 FAMKILKKRH 396 IVDTRQQEHI406 RSEKQIMQGA416 HSDFIVRLYR426 TFKDSKYLYM436 LMEACLGGEL 446 WTILRDRGSF456 EDSTTRFYTA466 CVVEAFAYLH476 SKGIIYRDLK486 PENLILDHRG 496 YAKLVDFGFA506 KKIGFGKKTW516 FCGTPEYVAP527 EIILNKGHDI537 SADYWSLGIL 547 MYELLTGSPP557 FSGPDPMKTY567 NIILRGIDMI577 EFPKKIAKNA587 ANLIKKLCRD 597 NPSERLGNLK607 NGVKDIQKHK617 WFEGFNWEGL627 RKGTLTPPII637 PSVASPTDTS 647 NFDSFPEDND657 EPPPDDNSGW667 DIDF
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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 .EE4 or .EE42 or .EE43 or :3EE4;style chemicals stick;color identity;select .A:366 or .A:367 or .A:368 or .A:369 or .A:370 or .A:371 or .A:372 or .A:373 or .A:374 or .A:388 or .A:390 or .A:392 or .A:400 or .A:402 or .A:405 or .A:406 or .A:409 or .A:422 or .A:438 or .A:439 or .A:440 or .A:441 or .A:445 or .A:488 or .A:489 or .A:491 or .A:501 or .A:502 or .A:504 or .A:505 or .A:649; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU366
4.000
GLY367
3.582
VAL368
3.541
GLY369
3.438
GLY370
3.348
PHE371
2.706
GLY372
3.667
ARG373
4.183
VAL374
3.359
ALA388
3.304
LYS390
4.297
LEU392
3.966
THR400
4.956
GLN402
3.314
HIS405
3.624
ILE406
3.243
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Ligand Name: PKG1|A activator 3 | Ligand Info | |||||
Structure Description | Co-structure of PKG1 regulatory domain with compound 33 | PDB:7SSB | ||||
Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [5] |
PDB Sequence |
STGLIKHTEY
227 MEFLKSVPTF237 QSLPEEILSK247 LADVLEETHY257 ENGEYIIRQG267 ARGDTFFIIS 277 KGTVNVTRED287 SDPVFLRTLG300 KGDWFGEKAL310 QGEDVRTANV320 IAAEAVTCLV 330 IDRDSFKHLI340 GGL
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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 .B4I or .B4I2 or .B4I3 or :3B4I;style chemicals stick;color identity;select .A:236 or .A:237 or .A:240 or .A:248 or .A:252 or .A:273 or .A:275 or .A:304 or .A:307 or .A:310 or .A:311 or .A:331 or .A:336 or .A:340; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: Deuterium Oxide | Ligand Info | |||||
Structure Description | Joint X-ray/neutron structure of PKGIbeta in complex with cGMP | PDB:4QXK | ||||
Method | Neutron diffraction | Resolution | 2.20 Å | Mutation | No | [2] |
PDB Sequence |
KHTEYMEFLK
232 SVPTFQSLPE242 EILSKLADVL252 EETHYENGEY262 IIRQGARGDT272 FFIISKGTVN 282 VTREDSPDPV294 FLRTLGKGDW304 FGEKALQGED314 VRTANVIAAE324 AVTCLVIDRD 334 SFKHLIGGLD344 DVSNKAY
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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 .DOD or .DOD2 or .DOD3 or :3DOD;style chemicals stick;color identity;select .A:223 or .A:224 or .A:225 or .A:226 or .A:227 or .A:228 or .A:230 or .A:232 or .A:233 or .A:234 or .A:235 or .A:236 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249 or .A:250 or .A:251 or .A:252 or .A:253 or .A:254 or .A:255 or .A:256 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261 or .A:262 or .A:263 or .A:264 or .A:265 or .A:266 or .A:267 or .A:268 or .A:269 or .A:270 or .A:271 or .A:272 or .A:274 or .A:276 or .A:277 or .A:278 or .A:279 or .A:280 or .A:282 or .A:284 or .A:285 or .A:286 or .A:287 or .A:288 or .A:289 or .A:292 or .A:293 or .A:294 or .A:295 or .A:296 or .A:297 or .A:298 or .A:299 or .A:300 or .A:301 or .A:302 or .A:303 or .A:304 or .A:305 or .A:306 or .A:307 or .A:308 or .A:309 or .A:310 or .A:311 or .A:312 or .A:313 or .A:314 or .A:315 or .A:316 or .A:317 or .A:318 or .A:319 or .A:321 or .A:323 or .A:324 or .A:325 or .A:326 or .A:327 or .A:330 or .A:331 or .A:332 or .A:333 or .A:334 or .A:335 or .A:336 or .A:337 or .A:338 or .A:339 or .A:340 or .A:341 or .A:342 or .A:343 or .A:344 or .A:345 or .A:346 or .A:347 or .A:348 or .A:349 or .A:350 or .A:351; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LYS223
1.943
HIS224
2.207
THR225
2.077
GLU226
2.456
TYR227
2.699
MET228
3.390
PHE230
3.599
LYS232
3.126
SER233
3.300
VAL234
3.566
PRO235
2.703
THR236
1.647
PHE237
2.955
GLN238
1.980
SER239
2.066
LEU240
2.417
PRO241
2.880
GLU242
1.785
GLU243
1.919
ILE244
2.088
LEU245
3.318
SER246
1.861
LYS247
2.320
LEU248
4.588
ALA249
2.086
ASP250
1.884
VAL251
2.562
LEU252
1.970
GLU253
2.412
GLU254
1.525
THR255
2.056
HIS256
2.128
TYR257
1.890
GLU258
1.644
ASN259
2.916
GLY260
4.647
GLU261
2.506
TYR262
1.999
ILE263
1.926
ILE264
2.516
ARG265
1.766
GLN266
2.078
GLY267
2.226
ALA268
2.812
ARG269
2.114
GLY270
3.325
ASP271
2.227
THR272
3.932
PHE274
3.109
ILE276
4.739
SER277
3.533
LYS278
1.778
GLY279
2.040
THR280
2.762
ASN282
3.022
THR284
3.629
ARG285
1.936
GLU286
2.359
ASP287
2.411
SER288
1.942
PRO289
2.625
ASP292
4.049
PRO293
2.565
VAL294
3.221
PHE295
3.248
LEU296
2.778
ARG297
2.400
THR298
2.375
LEU299
2.739
GLY300
2.900
LYS301
1.970
GLY302
2.301
ASP303
2.218
TRP304
1.913
PHE305
2.514
GLY306
4.535
GLU307
3.696
LYS308
2.741
ALA309
2.626
LEU310
2.009
GLN311
2.177
GLY312
1.903
GLU313
2.127
ASP314
2.111
VAL315
1.743
ARG316
2.981
THR317
2.327
ALA318
4.626
ASN319
1.937
ILE321
4.092
ALA323
3.439
GLU324
2.096
ALA325
1.631
VAL326
3.482
THR327
2.127
VAL330
2.199
ILE331
2.293
ASP332
1.728
ARG333
1.819
ASP334
2.160
SER335
3.300
PHE336
2.615
LYS337
2.464
HIS338
1.772
LEU339
2.144
ILE340
3.259
GLY341
1.881
GLY342
1.799
LEU343
3.091
ASP344
3.216
ASP345
1.573
VAL346
2.940
SER347
2.273
ASN348
3.059
LYS349
1.859
ALA350
1.601
TYR351
2.083
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Ligand Name: (Rp)-cGMPS | Ligand Info | |||||
Structure Description | PKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with RP-cGMP | PDB:5L0N | ||||
Method | X-ray diffraction | Resolution | 1.28 Å | Mutation | No | [6] |
PDB Sequence |
GLIKHTEYME
229 FLKSVPTFQS239 LPEEILSKLA249 DVLEETHYEN259 GEYIIRQGAR269 GDTFFIISKG 279 TVNVTREDSP289 SEDPVFLRTL299 GKGDWFGEKA309 LQGEDVRTAN319 VIAAEAVTCL 329 VIDRDSFKHL339 IGGLDDV
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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 .6ZA or .6ZA2 or .6ZA3 or :36ZA;style chemicals stick;color identity;select .A:264 or .A:283 or .A:285 or .A:296 or .A:297 or .A:299 or .A:304 or .A:305 or .A:306 or .A:307 or .A:308 or .A:309 or .A:313 or .A:315 or .A:316 or .A:317 or .A:318 or .A:319 or .A:320; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 8-bromo-cGMP | Ligand Info | |||||
Structure Description | PKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP | PDB:5JAX | ||||
Method | X-ray diffraction | Resolution | 1.49 Å | Mutation | No | [7] |
PDB Sequence |
IKHTEYMEFL
231 KSVPTFQSLP241 EEILSKLADV251 LEETHYENGE261 YIIRQGARGD271 TFFIISKGTV 281 NVTREDSPSE291 DPVFLRTLGK301 GDWFGEKALQ311 GEDVRTANVI321 AAEAVTCLVI 331 DRDSFKHLIG341 GLDDVSNKAY351
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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 .6J7 or .6J72 or .6J73 or :36J7;style chemicals stick;color identity;select .A:264 or .A:283 or .A:285 or .A:296 or .A:297 or .A:299 or .A:304 or .A:305 or .A:306 or .A:307 or .A:308 or .A:309 or .A:310 or .A:315 or .A:316 or .A:317 or .A:318 or .A:319 or .A:320 or .A:351; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ILE264
2.785
VAL283
2.744
ARG285
3.095
LEU296
2.531
ARG297
2.103
LEU299
2.868
TRP304
4.764
PHE305
2.398
GLY306
1.862
GLU307
2.123
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Ligand Name: 8-Pcpt-cgmp | Ligand Info | |||||
Structure Description | PKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-pCPT-cGMP | PDB:5J48 | ||||
Method | X-ray diffraction | Resolution | 1.49 Å | Mutation | No | [7] |
PDB Sequence |
GSTGLIKHTE
226 YMEFLKSVPT236 FQSLPEEILS246 KLADVLEETH256 YENGEYIIRQ266 GARGDTFFII 276 SKGTVNVTRE286 DDPVFLRTLG300 KGDWFGEKAL310 QGEDVRTANV320 IAAEAVTCLV 330 IDRDSFKHLI340 GGLDDVSNKA350 Y
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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 .6FW or .6FW2 or .6FW3 or :36FW;style chemicals stick;color identity;select .A:264 or .A:283 or .A:285 or .A:296 or .A:297 or .A:299 or .A:304 or .A:305 or .A:306 or .A:307 or .A:308 or .A:309 or .A:310 or .A:315 or .A:316 or .A:317 or .A:318 or .A:319 or .A:320 or .A:349 or .A:351; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ILE264
2.604
VAL283
2.860
ARG285
2.544
LEU296
2.618
ARG297
2.114
LEU299
2.616
TRP304
2.599
PHE305
2.564
GLY306
2.066
GLU307
2.626
LYS308
2.227
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Ligand Name: 1,N-(2-Phenyl-1,2-ethenediyl)guanosine 3',5'-phosphoric acid | Ligand Info | |||||
Structure Description | PKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with PET-cGMP | PDB:5JD7 | ||||
Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [7] |
PDB Sequence |
IKHTEYMEFL
231 KSVPTFQSLP241 EEILSKLADV251 LEETHYENGE261 YIIRQGARGD271 TFFIISKGTV 281 NVTREDEDPV294 FLRTLGKGDW304 FGEKALQGED314 VRTANVIAAE324 AVTCLVIDRD 334 SFKHLIGGLD344 DVSNKAY
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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 .6JR or .6JR2 or .6JR3 or :36JR;style chemicals stick;color identity;select .A:264 or .A:283 or .A:285 or .A:296 or .A:297 or .A:299 or .A:304 or .A:305 or .A:306 or .A:307 or .A:308 or .A:309 or .A:310 or .A:315 or .A:316 or .A:317 or .A:318 or .A:319 or .A:320 or .A:351; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ILE264
2.774
VAL283
2.409
ARG285
3.191
LEU296
2.500
ARG297
2.102
LEU299
2.471
TRP304
4.219
PHE305
2.327
GLY306
1.989
GLU307
1.858
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References | Top | ||||
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REF 1 | Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain | ||||
REF 2 | Neutron diffraction reveals hydrogen bonds critical for cGMP-selective activation: insights for cGMP-dependent protein kinase agonist design. Biochemistry. 2014 Nov 4;53(43):6725-7. | ||||
REF 3 | Structural basis for cyclic-nucleotide selectivity and cGMP-selective activation of PKG I. Structure. 2014 Jan 7;22(1):116-24. | ||||
REF 4 | Structural basis for selective inhibition of human PKG IAlpha by the balanol-like compound N46. J Biol Chem. 2018 Jul 13;293(28):10985-10992. | ||||
REF 5 | Optimization and Mechanistic Investigations of Novel Allosteric Activators of PKG1Alpha. J Med Chem. 2022 Aug 11;65(15):10318-10340. | ||||
REF 6 | Structure of PKG I CNB-B bound to RP-cGMP | ||||
REF 7 | Structural Basis of Analog Specificity in PKG I and II. ACS Chem Biol. 2017 Sep 15;12(9):2388-2398. |
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