Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T23606 Target Info
Target Name Protein kinase G2 (PRKG2)
Synonyms cGMP-dependent protein kinase II; cGMP-dependent protein kinase 2; cGKII; cGK2; cGK 2; PRKGR2
Target Type Literature-reported Target
Gene Name PRKG2
UniProt ID
KGP2_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Cyclic Guanosine Monophosphate Ligand Info
Structure Description PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with cGMP PDB:5BV6
Method X-ray diffraction Resolution 1.94 Å Mutation No [1]
PDB Sequence
TAQARDEQYR
278
NFLRSVSLLK
288
NLPEDKLTKI
298
IDCLEVEYYD
308
KGDYIIREGE
318

EGSTFFILAK
328
GKVKVTQSTE
338
GHDQPQLIKT
348
LQKGEYFGEK
358
ALISDDVRSA
368

NIIAEENDVA
378
CLVIDRETFN
388
QTVGTFEELQ
398
KYLEGYVANL
408
NRDDEKRHAK
418
Residue
Distance (Å)
ILE314
3.906
VAL333
3.826
GLN335
3.535
ILE346
4.103
LYS347
3.183
TYR354
4.584
PHE355
3.280
GLY356
2.968
GLU357
2.647
LYS358
3.295
ALA359
3.015
Residue
Distance (Å)
VAL365
4.415
ARG366
2.907
SER367
2.765
ALA368
3.519
ILE370
3.536
TYR404
4.832
LEU408
3.800
ASP411
4.079
ASP412
2.760
ARG415
3.236
Ligand Name: Cyclic Guanosine Monophosphate Ligand Info
Structure Description PKG II's Amino Terminal Cyclic Nucleotide Binding Domain (CNB-A) in a complex with cGMP PDB:5C8W
Method X-ray diffraction Resolution 1.80 Å Mutation No [1]
PDB Sequence
RKDSSEKKLI
159
TDALNKNQFL
169
KRLDPQQIKD
179
MVECMYGRNY
189
QQGSYIIKQG
199

EPGNHIFVLA
209
EGRLEVFQGE
219
KLLSSIPMWT
229
TFGELAILYN
239
CTRTASVKAI
249

TNVKTWALDR
259
EVFQNIMRRT
269
Residue
Distance (Å)
ILE196
2.867
VAL215
2.839
GLN217
4.256
LEU222
3.172
SER223
3.185
ILE225
3.447
THR230
4.715
PHE231
2.860
GLY232
2.218
Residue
Distance (Å)
GLU233
2.700
LEU234
2.784
ALA235
2.150
ILE236
4.393
THR241
4.782
ARG242
2.126
THR243
1.982
ALA244
3.217
VAL246
3.327
Ligand Name: [3H]cAMP Ligand Info
Structure Description PKG II's Amino Terminal Cyclic Nucleotide Binding Domain (CNB-A) in a complex with cAMP PDB:5C6C
Method X-ray diffraction Resolution 2.05 Å Mutation No [1]
PDB Sequence
RKDSSEKKLI
159
TDALNKNQFL
169
KRLDPQQIKD
179
MVECMYGRNY
189
QQGSYIIKQG
199

EPGNHIFVLA
209
EGRLEVFQGE
219
KLLSSIPMWT
229
TFGELAILYN
239
CTRTASVKAI
249

TNVKTWALDR
259
EVFQNIMRR
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:196 or .A:215 or .A:222 or .A:223 or .A:230 or .A:231 or .A:232 or .A:233 or .A:234 or .A:235 or .A:236 or .A:241 or .A:242 or .A:243 or .A:244 or .A:246; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE196
3.733
VAL215
3.924
LEU222
4.197
SER223
3.582
THR230
4.731
PHE231
3.525
GLY232
3.051
GLU233
2.719
Residue
Distance (Å)
LEU234
3.523
ALA235
3.007
ILE236
4.686
THR241
4.334
ARG242
2.857
THR243
2.803
ALA244
3.474
VAL246
3.933
Ligand Name: 3,6,9,12,15,18,21,24-Octaoxahexacosan-1-OL Ligand Info
Structure Description PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP PDB:5JIX
Method X-ray diffraction Resolution 1.47 Å Mutation No [2]
PDB Sequence
TAQARDEQYR
278
NFLRSVSLLK
288
NLPEDKLTKI
298
IDCLEVEYYD
308
KGDYIIREGE
318

EGSTFFILAK
328
GKVKVTQSTE
338
GHDQPQLIKT
348
LQKGEYFGEK
358
ALISDDVRSA
368

NIIAEENDVA
378
CLVIDRETFN
388
QTVGTFEELQ
398
KYLEGYVANL
408
NRDDEKRHAK
418
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PE5 or .PE52 or .PE53 or :3PE5;style chemicals stick;color identity;select .A:309 or .A:310 or .A:332 or .A:334 or .A:343 or .A:345 or .A:348 or .A:371 or .A:372 or .A:373 or .A:374; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS309
3.387
GLY310
2.605
LYS332
1.728
THR334
2.972
PRO343
4.971
LEU345
2.451
Residue
Distance (Å)
THR348
2.797
ILE371
2.632
ALA372
3.512
GLU373
2.133
GLU374
4.807
Ligand Name: 8-bromo-cGMP Ligand Info
Structure Description PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP PDB:5JIX
Method X-ray diffraction Resolution 1.47 Å Mutation No [2]
PDB Sequence
TAQARDEQYR
278
NFLRSVSLLK
288
NLPEDKLTKI
298
IDCLEVEYYD
308
KGDYIIREGE
318

EGSTFFILAK
328
GKVKVTQSTE
338
GHDQPQLIKT
348
LQKGEYFGEK
358
ALISDDVRSA
368

NIIAEENDVA
378
CLVIDRETFN
388
QTVGTFEELQ
398
KYLEGYVANL
408
NRDDEKRHAK
418
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:314 or .A:333 or .A:335 or .A:346 or .A:347 or .A:349 or .A:354 or .A:355 or .A:356 or .A:357 or .A:358 or .A:359 or .A:360 or .A:365 or .A:366 or .A:367 or .A:368 or .A:369 or .A:370 or .A:404 or .A:408 or .A:409 or .A:411 or .A:412 or .A:415; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE314
2.467
VAL333
3.062
GLN335
2.352
ILE346
3.145
LYS347
2.574
LEU349
3.017
TYR354
4.236
PHE355
2.526
GLY356
2.141
GLU357
2.405
LYS358
2.601
ALA359
2.267
LEU360
4.703
Residue
Distance (Å)
VAL365
4.283
ARG366
1.964
SER367
1.816
ALA368
2.379
ASN369
4.347
ILE370
2.589
TYR404
3.100
LEU408
2.384
ASN409
4.975
ASP411
3.620
ASP412
1.786
ARG415
2.257
Ligand Name: 8-Pcpt-cgmp Ligand Info
Structure Description PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-pCPT-cGMP PDB:5JIZ
Method X-ray diffraction Resolution 1.50 Å Mutation No [3]
PDB Sequence
STAQARDEQY
277
RNFLRSVSLL
287
KNLPEDKLTK
297
IIDCLEVEYY
307
DKGDYIIREG
317

EEGSTFFILA
327
KGKVKVTQST
337
EGHDQPQLIK
347
TLQKGEYFGE
357
KALISDDVRS
367

ANIIAEENDV
377
ACLVIDRETF
387
NQTVGTFEEL
397
QKYLEGYVAN
407
LNRDDEKRHA
417

K
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:314 or .A:320 or .A:323 or .A:333 or .A:335 or .A:346 or .A:347 or .A:349 or .A:354 or .A:355 or .A:356 or .A:357 or .A:358 or .A:359 or .A:360 or .A:365 or .A:366 or .A:367 or .A:368 or .A:369 or .A:370 or .A:399 or .A:401 or .A:402 or .A:403 or .A:404 or .A:405 or .A:406 or .A:408 or .A:411 or .A:412 or .A:415; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE314
2.894
GLY320
4.865
PHE323
4.413
VAL333
2.846
GLN335
2.465
ILE346
2.885
LYS347
2.883
LEU349
3.005
TYR354
2.687
PHE355
2.589
GLY356
1.940
GLU357
1.835
LYS358
2.655
ALA359
2.019
LEU360
4.645
VAL365
4.303
Residue
Distance (Å)
ARG366
1.943
SER367
1.681
ALA368
2.439
ASN369
4.243
ILE370
2.678
LYS399
3.305
LEU401
3.276
GLU402
2.872
GLY403
3.286
TYR404
2.767
VAL405
4.276
ALA406
3.286
LEU408
2.313
ASP411
3.680
ASP412
1.917
ARG415
2.513
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Deuterium Oxide Ligand Info
Structure Description Joint X-ray/neutron structure of PKG II CNB-B domain in complex with 8-pCPT-cGMP PDB:6BQ8
Method X-ray diffraction Resolution 2.00 Å Mutation No [4]
PDB Sequence
TAQARDEQYR
278
NFLRSVSLLK
288
NLPEDKLTKI
298
IDCLEVEYYD
308
KGDYIIREGE
318

EGSTFFILAK
328
GKVKVTQSTE
338
GHDQPQLIKT
348
LQKGEYFGEK
358
ALISDDVRSA
368

NIIAEENDVA
378
CLVIDRETFN
388
QTVGTFEELQ
398
KYLEGYVANL
408
NRDDEKRHAK
418
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:270 or .A:271 or .A:273 or .A:274 or .A:275 or .A:278 or .A:279 or .A:282 or .A:285 or .A:286 or .A:287 or .A:288 or .A:289 or .A:290 or .A:291 or .A:292 or .A:295 or .A:296 or .A:298 or .A:299 or .A:300 or .A:301 or .A:302 or .A:303 or .A:305 or .A:310 or .A:311 or .A:312 or .A:313 or .A:314 or .A:315 or .A:316 or .A:318 or .A:319 or .A:320 or .A:321 or .A:322 or .A:324 or .A:327 or .A:328 or .A:329 or .A:330 or .A:332 or .A:334 or .A:335 or .A:336 or .A:337 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:351 or .A:353 or .A:354 or .A:355 or .A:358 or .A:359 or .A:360 or .A:362 or .A:363 or .A:364 or .A:365 or .A:366 or .A:367 or .A:369 or .A:371 or .A:374 or .A:375 or .A:376 or .A:377 or .A:381 or .A:384 or .A:388 or .A:392 or .A:394 or .A:395 or .A:396 or .A:397 or .A:398 or .A:399 or .A:400 or .A:402 or .A:403 or .A:404 or .A:405 or .A:408 or .A:409 or .A:411 or .A:412 or .A:414 or .A:415; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ALA270
2.632
GLN271
4.333
ARG273
1.742
ASP274
2.289
GLU275
2.918
ARG278
1.902
ASN279
2.539
ARG282
2.220
SER285
3.317
LEU286
1.967
LEU287
3.194
LYS288
3.373
ASN289
2.093
LEU290
3.502
PRO291
4.099
GLU292
2.215
LEU295
3.387
THR296
4.731
ILE298
4.629
ILE299
2.387
ASP300
2.749
CYS301
3.530
LEU302
1.824
GLU303
3.833
GLU305
3.981
GLY310
2.266
ASP311
4.447
TYR312
2.524
ILE313
4.540
ILE314
2.580
ARG315
2.894
GLU316
2.267
GLU318
1.803
GLU319
2.876
GLY320
2.188
SER321
1.900
THR322
1.644
PHE324
2.823
ALA327
4.907
LYS328
2.467
GLY329
2.181
LYS330
2.177
LYS332
1.781
THR334
2.011
GLN335
4.075
SER336
2.153
THR337
4.268
HIS340
2.309
ASP341
4.334
Residue
Distance (Å)
GLN342
1.648
PRO343
2.370
GLN344
2.206
LEU345
2.731
ILE346
4.207
LYS347
2.503
THR348
1.895
LEU349
3.555
LYS351
2.971
GLU353
2.559
TYR354
2.011
PHE355
4.541
LYS358
2.065
ALA359
2.215
LEU360
3.005
SER362
1.760
ASP363
2.500
ASP364
2.025
VAL365
1.765
ARG366
2.078
SER367
2.162
ASN369
1.834
ILE371
2.463
GLU374
2.056
ASN375
1.949
ASP376
2.845
VAL377
3.420
VAL381
3.214
ARG384
2.146
ASN388
4.399
GLY392
4.410
PHE394
2.745
GLU395
2.507
GLU396
2.615
LEU397
2.248
GLN398
1.968
LYS399
2.103
TYR400
3.660
GLU402
1.627
GLY403
4.873
TYR404
2.154
VAL405
3.584
LEU408
2.634
ASN409
1.838
ASP411
1.766
ASP412
4.198
LYS414
1.745
ARG415
2.506
References  Top
REF 1 Structural Basis of Cyclic Nucleotide Selectivity in cGMP-dependent Protein Kinase II. J Biol Chem. 2016 Mar 11;291(11):5623-5633.
REF 2 Structural Basis of Analog Specificity in PKG I and II. ACS Chem Biol. 2017 Sep 15;12(9):2388-2398.
REF 3 PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-pCPT-cGMP
REF 4 Neutron Crystallography Detects Differences in Protein Dynamics: Structure of the PKG II Cyclic Nucleotide Binding Domain in Complex with an Activator. Biochemistry. 2018 Mar 27;57(12):1833-1837.

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