Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
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
KGP1_HUMAN
Ligand General Information  Top
Ligand Name Cyclic Guanosine Monophosphate Ligand Info
Canonical SMILES C1C2C(C(C(O2)N3C=NC4=C3N=C(NC4=O)N)O)OP(=O)(O1)O
InChI 1S/C10H12N5O7P/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6-3(21-9)1-20-23(18,19)22-6/h2-3,5-6,9,16H,1H2,(H,18,19)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKey ZOOGRGPOEVQQDX-UUOKFMHZSA-N
PubChem Compound ID 135398570
Drug Binding Sites of Target  Top
PDB ID: 4Z07      Co-crystal structure of the tandem CNB (CNB-A/B) domains of human PKG I beta with cGMP
Method X-ray diffraction Resolution 2.50 Å Mutation No [1]
PDB Sequence
SHVTLPFYPK
101
SPQSKDLIKE
111
AILDNDFMKN
121
LELSQIQEIV
131
DCMYPVEYGK
141

DSCIIKEGDV
151
GSLVYVMEDG
161
KVEVTKEGVK
171
LCTMGPGKVF
181
GELAILYNCT
191

RTATVKTLVN
201
VKLWAIDRQC
211
FQTIMMRTGL
221
IKHTEYMEFL
231
KSVPTFQSLP
241

EEILSKLADV
251
LEETHYENGE
261
YIIRQGARGD
271
TFFIISKGTV
281
NVTREDSPSE
291

DPVFLRTLGK
301
GDWFGEKALQ
311
GEDVRTANVI
321
AAEAVTCLVI
331
DRDSFKHLIG
341

GLDDVSNKAY
351
Residue
Distance (Å)
ILE146
3.809
VAL165
3.752
LYS167
4.506
LEU172
3.338
CYS173
3.663
MET175
3.905
VAL180
4.394
PHE181
3.357
GLY182
2.993
GLU183
2.429
LEU184
3.421
ALA185
2.863
ILE186
4.805
THR191
4.566
ARG192
2.753
THR193
2.589
ALA194
3.478
THR195
4.946
VAL196
3.791
Residue
Distance (Å)
ILE264
3.738
VAL283
3.589
ARG285
3.581
LEU296
3.351
ARG297
2.926
LEU299
4.517
TRP304
4.629
PHE305
3.193
GLY306
2.840
GLU307
2.389
LYS308
3.268
ALA309
2.871
LEU310
4.817
VAL315
4.303
ARG316
2.894
THR317
2.509
ALA318
3.499
VAL320
3.508
TYR351
3.029
PDB ID: 4KU7      Structures of PKGI Reveal a cGMP-Selective Activation Mechanism
Method X-ray diffraction Resolution 1.65 Å Mutation No [2]
PDB Sequence
KHTEYMEFLK
232
SVPTFQSLPE
242
EILSKLADVL
252
EETHYENGEY
262
IIRQGARGDT
272

FFIISKGTVN
282
VTREDPVFLR
297
TLGKGDWFGE
307
KALQGEDVRT
317
ANVIAAEAVT
327

CLVIDRDSFK
337
HLIGGLDDVS
347
NKAY
Residue
Distance (Å)
ILE264
3.679
VAL283
3.706
ARG285
4.258
LEU296
3.432
ARG297
2.717
LEU299
4.256
TRP304
4.656
PHE305
3.201
GLY306
2.818
Residue
Distance (Å)
GLU307
2.515
LYS308
3.343
ALA309
2.895
VAL315
4.268
ARG316
2.946
THR317
2.598
ALA318
3.444
VAL320
3.651
TYR351
3.137
PDB ID: 4QXK      Joint X-ray/neutron structure of PKGIbeta in complex with cGMP
Method Neutron diffraction Resolution 2.20 Å Mutation No [3]
PDB Sequence
KHTEYMEFLK
232
SVPTFQSLPE
242
EILSKLADVL
252
EETHYENGEY
262
IIRQGARGDT
272

FFIISKGTVN
282
VTREDSPDPV
294
FLRTLGKGDW
304
FGEKALQGED
314
VRTANVIAAE
324

AVTCLVIDRD
334
SFKHLIGGLD
344
DVSNKAY
Residue
Distance (Å)
ILE264
2.756
VAL283
2.954
ARG285
2.293
LEU296
2.857
ARG297
2.150
LEU299
2.211
TRP304
4.107
PHE305
2.357
GLY306
2.054
GLU307
1.726
LYS308
2.282
Residue
Distance (Å)
ALA309
1.918
LEU310
4.369
VAL315
4.367
ARG316
2.144
THR317
1.831
ALA318
2.452
ASN319
4.566
VAL320
2.579
LYS349
4.742
TYR351
2.821
PDB ID: 3OD0      Crystal structure of cGMP bound cGMP-dependent protein kinase(92-227)
Method X-ray diffraction Resolution 2.90 Å Mutation No [4]
PDB Sequence
SHVTLPFYPK
101
SPQSKDLIKE
111
AILDNDFMKN
121
LELSQIQEIV
131
DCMYPVEYGK
141

DSCIIKEGDV
151
GSLVYVMEDG
161
KVEVTKEGVK
171
LCTMGPGKVF
181
GELAILYNCT
191

RTATVKTLVN
201
VKLWAIDRQC
211
FQTIMMR
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:146 or .A:165 or .A:167 or .A:172 or .A:173 or .A:175 or .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:196; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE146
3.782
VAL165
3.974
LYS167
4.676
LEU172
3.437
CYS173
3.651
MET175
4.093
VAL180
4.125
PHE181
2.991
GLY182
2.823
Residue
Distance (Å)
GLU183
2.472
LEU184
3.343
ALA185
3.190
THR191
4.638
ARG192
2.624
THR193
2.691
ALA194
3.231
THR195
4.964
VAL196
4.040
References  Top
REF 1 Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation. Structure. 2016 May 3;24(5):710-720.
REF 2 Structural basis for cyclic-nucleotide selectivity and cGMP-selective activation of PKG I. Structure. 2014 Jan 7;22(1):116-24.
REF 3 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 4 Co-crystal structures of PKG Ibeta (92-227) with cGMP and cAMP reveal the molecular details of cyclic-nucleotide binding. PLoS One. 2011 Apr 19;6(4):e18413.

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