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Receptor
PDB id Resolution Class Description Source Keywords
3D4A 2.2 Å EC: 3.1.4.8 CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH 3'-GMP OBTAINED B DIFFUSION STREPTOMYCES AUREOFACIENS RIBONUCLEASE MONONUCLEOTIDE PROTEIN-MONONUCLEOTIDE COMPLEXHYDROLASE
Ref.: STRUCTURE OF RNASE SA2 COMPLEXES WITH MONONUCLEOTID ASPECTS OF CATALYTIC REACTION AND SUBSTRATE RECOGNI FEBS J. V. 276 4156 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3GP B:99;
Valid;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
SO4 A:98;
B:98;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DGY 1.8 Å EC: 3.1.4.8 CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH GUANOSINE-2'-CYCL STREPTOMYCES AUREOFACIENS RIBONUCLEASE HYDROLASE PROTEIN-MONONUCLEOTIDE COMPLEX GUA2-prime -MONOPHOSPHATE MONONUCLEOTIDE
Ref.: STRUCTURE OF RNASE SA2 COMPLEXES WITH MONONUCLEOTID ASPECTS OF CATALYTIC REACTION AND SUBSTRATE RECOGNI FEBS J. V. 276 4156 2009
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3DGY - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3D4A - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
3 3D5I - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
4 3DH2 - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3DGY - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3D4A - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
3 3D5I - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
4 3DH2 - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
5 2SAR - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
6 1RSN - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
7 1GMR - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
8 1GMP - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
9 1RGE - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3DGY - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3D4A - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
3 3D5I - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
4 3DH2 - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
5 2SAR - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
6 1RSN - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
7 1GMR - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
8 1GMP - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
9 1RGE - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3GP; Similar ligands found: 102
No: Ligand ECFP6 Tc MDL keys Tc
1 3GP 1 1
2 G3D 0.753086 0.959459
3 2GP 0.733333 0.959459
4 GMP 0.704225 0.853333
5 G4P 0.674419 0.959459
6 G 0.65 0.959459
7 5GP 0.65 0.959459
8 0O2 0.644444 0.959459
9 GDP 0.611765 0.946667
10 GNH 0.604651 0.934211
11 GCP G 0.602151 0.945946
12 GP3 0.6 0.922078
13 GSP 0.595506 0.898734
14 GP2 0.593023 0.910256
15 GPG 0.591398 0.935065
16 GTP 0.590909 0.946667
17 G2P 0.577778 0.910256
18 G G 0.57732 0.922078
19 G U34 0.576923 0.8875
20 G U 0.576923 0.898734
21 GMV 0.573034 0.922078
22 ALF 5GP 0.573034 0.864198
23 P2G 0.571429 0.932432
24 GDC 0.56701 0.935065
25 GDD 0.56701 0.935065
26 GKE 0.56701 0.935065
27 G1R 0.566667 0.934211
28 GCP 0.566667 0.922078
29 G C 0.566038 0.898734
30 GAV 0.565217 0.910256
31 G A A A 0.560748 0.922078
32 GNP 0.56044 0.922078
33 9GM 0.56044 0.922078
34 P1G 0.55814 0.92
35 ALF GDP 0.536842 0.864198
36 GDP AF3 0.536842 0.864198
37 GDP ALF 0.536842 0.864198
38 G2R 0.53125 0.910256
39 A G 0.518182 0.909091
40 SGP 0.517241 0.871795
41 GDR 0.514852 0.910256
42 GFB 0.514852 0.910256
43 GKD 0.514563 0.935065
44 U A G G 0.513514 0.909091
45 YGP 0.51 0.876543
46 6CK 0.509804 0.8875
47 G3A 0.509804 0.922078
48 U2G 0.509259 0.911392
49 BGO 0.509259 0.898734
50 G G G RPC 0.509091 0.897436
51 DG 0.505747 0.909091
52 DGP 0.505747 0.909091
53 GH3 0.505263 0.946667
54 Y9Z 0.504951 0.878049
55 G5P 0.504854 0.922078
56 APC G U 0.504425 0.909091
57 GTG 0.5 0.8875
58 CG2 0.5 0.911392
59 3AM 0.5 0.90411
60 JB2 0.5 0.910256
61 GDX 0.495238 0.922078
62 GPD 0.495238 0.876543
63 GPX 0.494845 0.92
64 GDP 7MG 0.490385 0.886076
65 DGI 0.48913 0.897436
66 JB3 0.486239 0.898734
67 G G G C 0.482759 0.8875
68 GGM 0.482143 0.876543
69 A G C C 0.478632 0.886076
70 35G 0.478261 0.932432
71 C2E 0.478261 0.92
72 PCG 0.478261 0.932432
73 A G U 0.47619 0.8875
74 5GP 5GP 0.473118 0.906667
75 2MD 0.469027 0.845238
76 DGT 0.46875 0.897436
77 NGD 0.468468 0.910256
78 FEG 0.468468 0.855422
79 DG DG 0.465347 0.8875
80 ZGP 0.464286 0.845238
81 G C C C 0.46281 0.898734
82 A G U U 0.458015 0.8875
83 MGD 0.456897 0.845238
84 GPC 0.456897 0.878049
85 AKW 0.455357 0.843373
86 CAG 0.444444 0.835294
87 PGD O 0.442623 0.806818
88 DBG 0.434426 0.898734
89 G1R G1R 0.434426 0.875
90 TPG 0.434426 0.797753
91 UCG 0.430894 0.910256
92 MD1 0.429752 0.845238
93 PGD 0.429752 0.876543
94 G1G 0.425 0.876543
95 FE9 0.421488 0.755319
96 4BW 0.416667 0.92
97 1YD 0.416667 0.92
98 3ZE 0.410526 0.858974
99 CGP 0.410256 0.888889
100 DC DG 0.40678 0.865854
101 A3P 0.402174 0.891892
102 G4M 0.401515 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DGY; Ligand: 2GP; Similar sites found with APoc: 179
This union binding pocket(no: 1) in the query (biounit: 3dgy.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 3WV1 WHH None
2 5KK4 44E None
3 3DAK ANP None
4 5AVF TAU None
5 3VPD ANP None
6 1U1F 183 None
7 1OZH HE3 0.530035
8 1RDS GPC 2.06186
9 1Z08 GNP 2.06186
10 4YZN 4K5 2.06186
11 5TA6 79D 2.06186
12 5UR1 YY9 2.06186
13 3FC2 IBI 2.06186
14 3KV8 FAH 2.06186
15 4YNM SAM 2.06186
16 4AUA 4AU 2.06186
17 4RJK TDL 2.06186
18 3TKI S25 3.09278
19 2HY0 306 3.09278
20 1YZQ GNP 3.09278
21 4I6H 1C8 3.09278
22 1AFS NAP 3.09278
23 1E6E FAD 3.09278
24 4EWH T77 3.09278
25 3WCS MAN NAG GAL 3.09278
26 2J7T 274 3.09278
27 3APT FAD 3.09278
28 5EJL C2E 3.09278
29 1YC5 NCA 3.09278
30 1B55 4IP 4.12371
31 2F57 23D 4.12371
32 2R3A SAM 4.12371
33 5TZO 7V7 4.12371
34 5EYK 5U5 4.12371
35 5JGA 6KC 4.12371
36 3BC1 GNP 4.12371
37 4ASE AV9 4.12371
38 2HRL SIA GAL SIA BGC NGA CEQ 4.12371
39 4C2V YJA 4.12371
40 3SXS PP2 4.12371
41 1D1T NAD 4.12371
42 1EHI ADP 4.12371
43 5SVV FMN 4.12371
44 3QLM PLM 4.12371
45 6GIU L69 4.12371
46 5HPZ 68G 4.12371
47 4Y93 746 4.12371
48 4KS7 X4Z 5.15464
49 5XVG 8FX 5.15464
50 5WO4 B7V 5.15464
51 4QMN DB8 5.15464
52 1IOW PHY 5.15464
53 1IOW ADP 5.15464
54 3BLI ACO 5.15464
55 4U98 ACP 5.15464
56 3ORQ ADP 5.15464
57 4LFL TG6 5.15464
58 4AG8 AXI 5.15464
59 3KRO PPV 5.15464
60 3KRO IPE 5.15464
61 5YVT NAI 5.15464
62 3V4S ATP 5.15464
63 5MW8 ATP 5.15464
64 5MW4 5JU 5.15464
65 3V8S 0HD 5.15464
66 3VHE 42Q 5.15464
67 3IE3 N11 5.15464
68 2FB3 GTP 5.15464
69 4CDN FO1 5.15464
70 5DEY 59T 6.18557
71 2XK9 XK9 6.18557
72 6C1S EFV 6.18557
73 5HCY 60D 6.18557
74 4Y0X ADP 6.18557
75 2DT9 THR 6.18557
76 3UDZ ADP 6.18557
77 2X2M X2M 6.18557
78 4IZC 1GZ 6.18557
79 4O4F ATP 6.18557
80 4O4F IHP 6.18557
81 1PK8 ATP 6.18557
82 1S9D AFB 6.18557
83 1OIX GDP 6.28272
84 4A4X JUP 7.2165
85 1VJY 460 7.2165
86 5ZCT ANP 7.2165
87 5FFF NAP 7.2165
88 3E5A VX6 7.2165
89 5FEU NAP 7.2165
90 4I6G FAD 7.2165
91 4TMN 0PK 7.2165
92 5USZ SKE 7.2165
93 4Z4P SAH 7.2165
94 3MVH WFE 7.2165
95 2YAK OSV 7.2165
96 4GYI ADP 7.2165
97 1Z6Z NAP 7.2165
98 2OFV 242 7.2165
99 5UIU 8CG 7.2165
100 1CDO NAD 7.2165
101 5VCV 1N1 7.2165
102 1PVN MZP 8.24742
103 4EUU BX7 8.24742
104 3DR4 G4M 8.24742
105 1ZD9 GDP 8.24742
106 4LRJ ANP 8.24742
107 3HAV ATP 8.24742
108 4X7Q 3YR 8.24742
109 4IX4 ADP 8.24742
110 3AHW 2AM 9.27835
111 5TO8 7FM 9.27835
112 3H9R TAK 9.27835
113 6GIN IR2 9.27835
114 4PNI KQQ 9.27835
115 3W2E FAD 9.27835
116 3W2E NAD 9.27835
117 4WNP 3RJ 9.27835
118 5L0U 660 9.27835
119 2FV5 541 9.27835
120 4R57 ACO 9.27835
121 1RNT 2GP 10.3093
122 1FUT 2GP 10.3093
123 6FTB M0E 10.3093
124 4DXJ 0M9 10.3093
125 4CLI 5P8 10.3093
126 5WNL STU 10.3093
127 2WTX VDO 10.3093
128 2WTX UDP 10.3093
129 4DXJ IPE 10.3093
130 4FMU 0UM 10.3093
131 2Y6O 1N1 10.3093
132 3KFL ME8 10.3093
133 4LH7 1X8 10.3093
134 5QIN J2V 10.3093
135 1LRW PQQ 10.8434
136 2Q7D ANP 11.3402
137 2PUL ACP 11.3402
138 6FL8 TIY 11.3402
139 6FL8 ADP 11.3402
140 4NW6 2NS 11.3402
141 4XZ3 ACP 11.3402
142 2Z7R STU 11.3402
143 4CRL C1I 11.3402
144 3LQV ADE 11.3402
145 5V22 SAH 11.3402
146 3S6X SIA GAL BGC 11.3402
147 5BV3 M7G 11.3402
148 3FHR P4O 12.3711
149 6EJI UD2 12.3711
150 2XG5 EC5 12.3711
151 2XG5 EC2 12.3711
152 3AKK ADP 12.3711
153 2JLD AG1 13.4021
154 2PZI AXX 13.4021
155 3RWO GDP 13.4021
156 3FXU TSU 13.4021
157 4UCI SAM 13.4021
158 2XVD AS6 14.433
159 1S7G NAD 15.4639
160 2IO8 ADP 15.4639
161 4NFE BEN 16.4948
162 3LDW ZOL 16.4948
163 3LDW IPE 16.4948
164 3WVR AMP 16.4948
165 1YNH SUO 16.4948
166 5ODQ FAD 17.5258
167 1Z2P I3S 18.5567
168 1Z2P ACP 18.5567
169 4E1Z 0MX 19.5876
170 5B2E MQG 19.5876
171 4CNK FAD 20.6186
172 5LXT ACP 20.6186
173 3LXK MI1 22.6804
174 1OPK P16 22.6804
175 5VC5 96M 23.7113
176 5COU ATP 26.8041
177 4GJ3 0XP 27.8351
178 3KRL KRL 27.8351
179 5K2M ADP 30.9278
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