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Receptor
PDB id Resolution Class Description Source Keywords
5BV6 1.94 Å EC: 2.7.11.12 PKG II'S CARBOXYL TERMINAL CYCLIC NUCLEOTIDE BINDING DOMAIN A COMPLEX WITH CGMP HOMO SAPIENS CYCLIC GMP-DEPENDENT PROTEIN KINASE TYPE II TRANSFERASE
Ref.: STRUCTURAL BASIS OF CYCLIC NUCLEOTIDE SELECTIVITY I CGMP-DEPENDENT PROTEIN KINASE II. J.BIOL.CHEM. V. 291 5623 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
35G A:501;
Valid;
none;
Kd = 31 nM
345.205 C10 H12 N5 O7 P c1nc2...
CA A:504;
A:502;
Invalid;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
ACT A:503;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
NA A:505;
Invalid;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5BV6 1.94 Å EC: 2.7.11.12 PKG II'S CARBOXYL TERMINAL CYCLIC NUCLEOTIDE BINDING DOMAIN A COMPLEX WITH CGMP HOMO SAPIENS CYCLIC GMP-DEPENDENT PROTEIN KINASE TYPE II TRANSFERASE
Ref.: STRUCTURAL BASIS OF CYCLIC NUCLEOTIDE SELECTIVITY I CGMP-DEPENDENT PROTEIN KINASE II. J.BIOL.CHEM. V. 291 5623 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5BV6 Kd = 31 nM 35G C10 H12 N5 O7 P c1nc2c(n1[....
2 5JIX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 5BV6 Kd = 31 nM 35G C10 H12 N5 O7 P c1nc2c(n1[....
2 5JIX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4OFG - PCG C10 H12 N5 O7 P c1nc2c(n1[....
2 5JAX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
3 5J48 - 6FW C16 H15 Cl N5 O7 P S c1cc(ccc1S....
4 5KJY - CMP C10 H12 N5 O6 P c1nc(c2c(n....
5 5KJX - CMP C10 H12 N5 O6 P c1nc(c2c(n....
6 5KJZ - PCG C10 H12 N5 O7 P c1nc2c(n1[....
7 5T3N Kd = 9.1 nM 75G C10 H11 Cl N5 O5 P S c1nc2c(nc(....
8 5K8S Kd = 6 nM CMP C10 H12 N5 O6 P c1nc(c2c(n....
9 5BV6 Kd = 31 nM 35G C10 H12 N5 O7 P c1nc2c(n1[....
10 5JIX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 35G; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 35G 1 1
2 C2E 1 0.986111
3 PCG 1 1
4 4BW 0.806818 0.986111
5 1YD 0.806818 0.986111
6 5GP 5GP 0.743902 0.945205
7 4UR 0.731959 0.986111
8 6SW 0.627907 0.957747
9 1YC 0.616162 0.958333
10 6J7 0.58427 0.946667
11 CMP 0.534091 0.888889
12 2BA 0.534091 0.902778
13 GMP 0.53012 0.84
14 1SY 0.495575 0.986111
15 SGP 0.483871 0.835443
16 6SZ 0.483871 0.902778
17 3GP 0.478261 0.932432
18 1OR 0.474747 0.729412
19 G 0.468085 0.945946
20 5GP 0.468085 0.945946
21 7CH 0.467391 0.875
22 6SX 0.462366 0.847222
23 6JR 0.457944 0.930556
24 G2R 0.457143 0.897436
25 GPX 0.451923 0.906667
26 GP3 0.44898 0.934211
27 2GP 0.446809 0.92
28 GP2 0.444444 0.897436
29 GDP 0.444444 0.933333
30 GNH 0.44 0.921053
31 P2G 0.4375 0.893333
32 G2P 0.436893 0.897436
33 GMV 0.431373 0.909091
34 GTP 0.431373 0.933333
35 ALF 5GP 0.431373 0.851852
36 G1R 0.427184 0.921053
37 GCP 0.427184 0.909091
38 G3D 0.423077 0.945946
39 9GM 0.423077 0.909091
40 GSP 0.423077 0.886076
41 GNP 0.423077 0.909091
42 GDP AF3 0.420561 0.851852
43 G4P 0.415094 0.945946
44 GAV 0.415094 0.897436
45 P1G 0.414141 0.881579
46 Y9Z 0.410714 0.843373
47 GCP G 0.409091 0.906667
48 GDP ALF 0.407407 0.851852
49 ALF GDP 0.407407 0.851852
50 N6R 0.40708 0.818182
51 N6S 0.40708 0.818182
52 G G 0.40708 0.934211
53 G3A 0.403509 0.934211
54 YGP 0.401786 0.8875
55 GPG 0.4 0.922078
56 G5P 0.4 0.934211
57 0O2 0.4 0.945946
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5BV6; Ligand: 35G; Similar sites found with APoc: 206
This union binding pocket(no: 1) in the query (biounit: 5bv6.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA None
2 4POJ 2VP None
3 1C9K 5GP None
4 4M8E 29V None
5 4NAT ADP None
6 4NAT 2W5 None
7 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU None
8 2YVE MBT None
9 1MID LAP None
10 2V1O COA None
11 6CHP F0Y None
12 5NFB 8VT None
13 3FIU POP None
14 5L7G 6QE None
15 5HES 032 None
16 5N1X 8HH 1.69492
17 5IFK HPA 1.97368
18 3M3E GAL A2G NPO 1.97368
19 1QVJ RP5 1.97368
20 1AUA BOG 1.97368
21 4O4Z N2O 1.97368
22 3NV3 GAL NAG MAN 2.17391
23 1A78 TDG 2.23881
24 4YLZ LAT NAG GAL 2.63158
25 4CSD MFU 2.63158
26 4P5Z Q7M 2.63158
27 4IXW IXW 2.63158
28 3KVY URA 2.63158
29 3ORF NAD 2.63158
30 3FAL REA 2.63158
31 4Y8D 49J 2.85714
32 1SLT NDG GAL 2.98507
33 4AG8 AXI 3.28947
34 6CB2 OLC 3.28947
35 1T57 FMN 3.28947
36 3QH2 3NM 3.28947
37 4MRP GSH 3.94737
38 5EW9 5VC 3.94737
39 3THR C2F 3.94737
40 2WLG SOP 3.94737
41 3X1M COA 3.94737
42 1RRC ADP 3.94737
43 3TL1 JRO 3.94737
44 6APV 3L4 3.94737
45 3W54 RNB 3.94737
46 2XZ9 PYR 3.94737
47 2DW7 SRT 3.94737
48 5BTX CMP 4.10959
49 2QCX PF1 4.56274
50 5V4R MGT 4.60526
51 2P3I MNA 4.60526
52 5X80 SAL 4.60526
53 3CHT 4NB 4.60526
54 1KQR MNA 4.60526
55 5IH9 6BF 4.60526
56 2BP1 FLC 4.60526
57 2PTZ PAH 4.60526
58 5OES ADP 4.60526
59 1PVN MZP 4.60526
60 1NX4 AKG 4.60526
61 3VV1 GAL FUC 4.60526
62 6MDE MEV 4.60526
63 3BPX SAL 4.72973
64 1LTT GAL BGC 4.85437
65 1LT3 GAL BGC 4.85437
66 5EYK 5U5 5.08475
67 1Q19 SSC 5.26316
68 3NW7 LGV 5.26316
69 4XNV BUR 5.26316
70 2X1L ADN 5.26316
71 6BVM EBV 5.26316
72 5XJ7 87O 5.26316
73 5Z9S BGC 5.26316
74 3WV6 GAL BGC 5.26316
75 4XDA RIB 5.26316
76 1V0O INR 5.26316
77 5KL0 G16 5.26316
78 3O01 DXC 5.92105
79 1H82 GZZ 5.92105
80 3W5N RAM 5.92105
81 2DKD NG1 5.92105
82 5B0I BOG 5.92105
83 5MB4 NAG 5.92105
84 2V7O DRN 5.92105
85 1K0E TRP 5.92105
86 2IMP LAC 5.92105
87 1IS3 LAT 5.92593
88 4LIK CIT 6.57895
89 1UUY PPI 6.57895
90 4ZCW 4NG 6.57895
91 2V5E SCR 6.57895
92 1WNB BTL 6.57895
93 3E70 GDP 6.57895
94 2Q1H AS4 6.57895
95 2YFB SIN 6.57895
96 2ET1 GLV 6.57895
97 3KOX Z98 6.61157
98 4C2V YJA 6.81818
99 3GF2 SAL 6.84932
100 3RMK BML 7.22892
101 5N87 N66 7.23684
102 5BVE 4VG 7.23684
103 5GLT BGC GAL NAG GAL 7.23684
104 1RJW ETF 7.23684
105 2I6U NVA 7.23684
106 5Y80 IRE 7.43243
107 4YEE 4CQ 7.77778
108 4Z7X 3CX 7.89474
109 2BO4 FLC 7.89474
110 1FM9 9CR 7.89474
111 5W4W 9WG 7.89474
112 3KYQ DPV 7.89474
113 5DRB 5FJ 7.89474
114 3T03 3T0 7.89474
115 2P7Q GG6 8.27068
116 1VMK GUN 8.30325
117 5Y02 MXN 8.41121
118 1ZED PNP 8.55263
119 5YLT C7N 8.55263
120 1VBH PEP 8.55263
121 1RYO OXL 9.21053
122 1OPK P16 9.21053
123 5UR1 YY9 9.21053
124 4YZC STU 9.21053
125 2CYC TYR 9.21053
126 1EBG PAH 9.21053
127 5OLK DTP 9.21053
128 1DQN IMU 9.86842
129 4OGQ 7PH 9.86842
130 4H4D 10E 9.86842
131 5LX9 OLB 10.5263
132 4OB6 S2T 10.5263
133 3H9R TAK 10.5263
134 5JKG 6LF 11.1842
135 4X1B MLI 11.1842
136 2PVN P63 11.1842
137 5QIN J2V 11.1842
138 5C9J DAO 11.1842
139 5IM3 DTP 11.1842
140 3FJG 3PG 11.8421
141 1PK8 ATP 11.8421
142 4QXB OGA 11.8421
143 5JFS 6K0 11.8421
144 1I0B PEL 11.8421
145 5ML3 DL3 12.0805
146 2QE4 JJ3 12.5
147 4WHZ 3NL 12.5
148 3HW5 AMP 12.5
149 4TV1 36M 12.5
150 4CNO 9PY 12.5
151 3KP6 SAL 12.5828
152 1T0S BML 12.7907
153 3BZ3 YAM 13.1579
154 1EYQ NAR 13.1579
155 5YF9 NIO 13.1579
156 3SXS PP2 13.1579
157 1LOX RS7 13.1579
158 4D52 GIV 13.1579
159 4D52 GXL 13.1579
160 5ODQ 9SB 13.1579
161 6A5Y 9CR 14.4737
162 2XDQ MGX 14.4737
163 5E5U MLT 14.4737
164 2YMZ LAT 14.6154
165 2C3W GLC GLC GLC GLC 14.7059
166 5OCA 9QZ 15.1316
167 3LA3 2FT 15.1316
168 2FVK DUC 15.1316
169 3GGF GVD 15.1316
170 1Z0N BCD 15.625
171 4RW3 TDA 15.7895
172 2QF7 AGS 15.7895
173 2W3L DRO 15.9722
174 2F7A BEZ 16.4474
175 4XV1 904 17.1053
176 2F57 23D 17.7632
177 2XKO AKG 18.4211
178 2XHK AKG 18.4211
179 1LCF OXL 19.7368
180 5JGA 6KC 21.0526
181 5H5O PCG 21.7054
182 2XVD AS6 21.7105
183 1I7L ATP 24.3421
184 4AVB CMP 26.9737
185 1XPJ TLA 27.7778
186 4N9I PCG 28.9474
187 3I54 CMP 28.9474
188 4CYD CMP 28.9474
189 3I59 N6S 28.9474
190 3I59 N6R 28.9474
191 2XK9 XK9 28.9474
192 6AR9 3L4 29.6053
193 3G5D 1N1 30.9211
194 5NKB 8ZT 32.2368
195 4MUV PCG 32.3944
196 3KCC CMP 33.5526
197 2WEI VGG 33.5526
198 3IGO ANP 33.5526
199 1BYG STU 34.2105
200 2HK5 1BM 34.2105
201 3CF6 SP1 34.8684
202 3PNA CMP 38.1579
203 2PTM CMP 38.8158
204 4NVP 7CH 41.4474
205 1CX4 CMP 47.3684
206 1NE6 SP1 47.3684
207 3OF1 CMP 50
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