Receptor
PDB id Resolution Class Description Source Keywords
3DH2 2.25 Å EC: 3.1.4.8 CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH GUANOSINE-3'-CYCL PREPARED BY COCRYSTALLIZATION STREPTOMYCES AUREOFACIENS RIBONUCLEASE HYDROLASE PROTEIN-MONONUCLEOTIDE COMPLEX GUA3-prime -MONOPHOSPHATE MONONUCLEOTIDE COCRYSTALLIZATION
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 A:98;
B:98;
C:98;
D:98;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
BGC A:99;
B:99;
C:99;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
180.156 C6 H12 O6 C([C@...
SO4 A:100;
Invalid;
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: 103
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 5GP 0.65 0.959459
7 G 0.65 0.959459
8 0O2 0.644444 0.959459
9 GDP 0.611765 0.946667
10 GNH 0.604651 0.934211
11 G G 0.602151 0.909091
12 GP3 0.6 0.922078
13 GDP MG 0.597701 0.897436
14 GSP 0.595506 0.898734
15 GP2 0.593023 0.910256
16 GPG 0.591398 0.935065
17 GTP 0.590909 0.946667
18 GDP BEF 0.590909 0.875
19 G2P 0.577778 0.910256
20 G U34 0.576923 0.8875
21 ALF 5GP 0.573034 0.864198
22 GMV 0.573034 0.922078
23 P2G 0.571429 0.932432
24 BEF GDP 0.571429 0.864198
25 GDC 0.56701 0.935065
26 GDD 0.56701 0.935065
27 GKE 0.56701 0.935065
28 G1R 0.566667 0.934211
29 GCP 0.566667 0.922078
30 G C 0.566038 0.898734
31 GAV 0.565217 0.910256
32 G A A A 0.560748 0.922078
33 GNP 0.56044 0.922078
34 G G U 0.56 0.934211
35 P1G 0.55814 0.92
36 GTP MG 0.554348 0.897436
37 GCP G 0.548387 0.909091
38 GDP ALF 0.536842 0.864198
39 GDP AF3 0.536842 0.864198
40 G2R 0.53125 0.910256
41 SGP 0.517241 0.871795
42 GFB 0.514852 0.910256
43 GDR 0.514852 0.910256
44 GKD 0.514563 0.935065
45 U A G G 0.513514 0.909091
46 YGP 0.51 0.876543
47 G3A 0.509804 0.922078
48 6CK 0.509804 0.8875
49 BGO 0.509259 0.898734
50 U2G 0.509259 0.911392
51 G G G RPC 0.509091 0.897436
52 DG 0.505747 0.909091
53 DGP 0.505747 0.909091
54 GH3 0.505263 0.946667
55 Y9Z 0.504951 0.878049
56 G5P 0.504854 0.922078
57 APC G U 0.504425 0.909091
58 GTG 0.5 0.8875
59 CG2 0.5 0.911392
60 JB2 0.5 0.910256
61 3AM 0.5 0.90411
62 GPD 0.495238 0.876543
63 GDX 0.495238 0.922078
64 GPX 0.494845 0.92
65 GDP 7MG 0.490385 0.886076
66 DGI 0.48913 0.897436
67 JB3 0.486239 0.898734
68 G G G C 0.482759 0.8875
69 GGM 0.482143 0.876543
70 A G C C 0.478632 0.886076
71 PCG 0.478261 0.932432
72 35G 0.478261 0.932432
73 C2E 0.478261 0.92
74 A G U 0.47619 0.8875
75 5GP 5GP 0.473118 0.906667
76 2MD 0.469027 0.845238
77 DGT 0.46875 0.897436
78 FEG 0.468468 0.855422
79 NGD 0.468468 0.910256
80 DG DG 0.465347 0.8875
81 ZGP 0.464286 0.845238
82 G C C C 0.46281 0.898734
83 GPC 0.456897 0.878049
84 MGD 0.456897 0.845238
85 U G A 0.449612 0.8875
86 CAG 0.444444 0.835294
87 PGD O 0.442623 0.806818
88 I2C FE2 CMO CMO 0.440678 0.786517
89 G1R G1R 0.434426 0.875
90 TPG 0.434426 0.797753
91 DBG 0.434426 0.898734
92 UCG 0.430894 0.910256
93 MD1 0.429752 0.845238
94 PGD 0.429752 0.876543
95 G1G 0.425 0.876543
96 FE9 0.421488 0.755319
97 1YD 0.416667 0.92
98 4BW 0.416667 0.92
99 3ZE 0.410526 0.858974
100 CGP 0.410256 0.888889
101 DC DG 0.40678 0.865854
102 A3P 0.402174 0.891892
103 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: 155
This union binding pocket(no: 1) in the query (biounit: 3dgy.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3WV1 WHH 0.01111 0.4488 None
2 3DAK ANP 0.01165 0.41747 None
3 5AVF TAU 0.007883 0.41471 None
4 3VPD ANP 0.02174 0.40916 None
5 1OZH HE3 0.04908 0.42055 0.530035
6 1RDS GPC 0.000008975 0.57209 2.06186
7 1Z08 GNP 0.006146 0.44037 2.06186
8 4BKJ STI 0.01042 0.43689 2.06186
9 4YZN 4K5 0.007328 0.43608 2.06186
10 5TA6 79D 0.01597 0.42347 2.06186
11 5UR1 YY9 0.02851 0.4141 2.06186
12 4YNM SAM 0.01477 0.41229 2.06186
13 4AUA 4AU 0.01762 0.4044 2.06186
14 4RJK TDL 0.04569 0.40177 2.06186
15 3TKI S25 0.0157 0.44509 3.09278
16 2HY0 306 0.002609 0.4449 3.09278
17 1YZQ GNP 0.01867 0.41895 3.09278
18 1AFS NAP 0.03754 0.40691 3.09278
19 1E6E FAD 0.04723 0.40639 3.09278
20 4EWH T77 0.03029 0.40637 3.09278
21 3WCS MAN NAG GAL 0.01508 0.40411 3.09278
22 2J7T 274 0.03979 0.40399 3.09278
23 1YC5 NCA 0.04471 0.40022 3.09278
24 2F57 23D 0.001216 0.46264 4.12371
25 2R3A SAM 0.002249 0.45595 4.12371
26 5EYK 5U5 0.01482 0.42597 4.12371
27 5JGA 6KC 0.01744 0.42527 4.12371
28 3BC1 GNP 0.01568 0.42146 4.12371
29 4ASE AV9 0.01636 0.42116 4.12371
30 2HRL SIA GAL SIA BGC NGA CEQ 0.006984 0.41909 4.12371
31 4C2V YJA 0.02447 0.41634 4.12371
32 3SXS PP2 0.01453 0.41531 4.12371
33 1D1T NAD 0.03646 0.40694 4.12371
34 1EHI ADP 0.02113 0.40576 4.12371
35 5SVV FMN 0.02361 0.40443 4.12371
36 1B55 4IP 0.001275 0.40216 4.12371
37 4Y93 746 0.03493 0.40199 4.12371
38 4KS7 X4Z 0.001168 0.47638 5.15464
39 2X4Z X4Z 0.00274 0.47104 5.15464
40 5HX8 66P 0.005223 0.44712 5.15464
41 4QMN DB8 0.0107 0.44043 5.15464
42 5GRF ADP 0.01189 0.43149 5.15464
43 1IOW PHY 0.02654 0.41896 5.15464
44 1IOW ADP 0.02654 0.41896 5.15464
45 3BLI ACO 0.01554 0.41861 5.15464
46 4U98 ACP 0.01019 0.41787 5.15464
47 3ORQ ADP 0.01464 0.41674 5.15464
48 3PE2 E1B 0.04146 0.41492 5.15464
49 4LFL TG6 0.009712 0.41474 5.15464
50 4AG8 AXI 0.03255 0.4127 5.15464
51 3KRO PPV 0.01514 0.40912 5.15464
52 3KRO IPE 0.01958 0.40912 5.15464
53 3V4S ATP 0.02477 0.40494 5.15464
54 5MW8 ATP 0.02739 0.40474 5.15464
55 5MW4 5JU 0.04669 0.40457 5.15464
56 3V8S 0HD 0.01946 0.40404 5.15464
57 3VHE 42Q 0.03899 0.40317 5.15464
58 3IE3 GSH 0.03925 0.40315 5.15464
59 3IE3 N11 0.03925 0.40315 5.15464
60 2FB3 GTP 0.04352 0.40206 5.15464
61 4CDN FO1 0.0259 0.40188 5.15464
62 5DEY 59T 0.009471 0.4568 6.18557
63 2XK9 XK9 0.005556 0.45543 6.18557
64 5HCY 60D 0.01588 0.43683 6.18557
65 4Y0X ADP 0.007272 0.42347 6.18557
66 2DT9 THR 0.006073 0.42044 6.18557
67 2GU8 796 0.04335 0.4193 6.18557
68 3UDZ ADP 0.01281 0.41716 6.18557
69 2X2M X2M 0.01618 0.41624 6.18557
70 4IZC 1GZ 0.02909 0.41513 6.18557
71 4O4F IHP 0.02938 0.40753 6.18557
72 4O4F ATP 0.02771 0.40753 6.18557
73 1S9D AFB 0.01651 0.40284 6.18557
74 1PK8 ATP 0.03584 0.40233 6.18557
75 3OOI SAM 0.02627 0.40161 6.18557
76 1OIX GDP 0.009568 0.43329 6.28272
77 4A4X JUP 0.002974 0.46067 7.2165
78 5EW9 5VC 0.02117 0.45931 7.2165
79 4TMN 0PK 0.02059 0.41527 7.2165
80 4BHN BH9 0.01504 0.41441 7.2165
81 1VJY 460 0.02977 0.41181 7.2165
82 5USZ SKE 0.02494 0.41169 7.2165
83 4Z4P SAH 0.01498 0.41034 7.2165
84 4AXD ANP 0.04561 0.40799 7.2165
85 3MVH WFE 0.03301 0.40782 7.2165
86 2YAK OSV 0.03389 0.40741 7.2165
87 1Z6Z NAP 0.04496 0.40263 7.2165
88 2OFV 242 0.04989 0.4026 7.2165
89 5UIU 8CG 0.04248 0.40092 7.2165
90 1CDO NAD 0.04001 0.40089 7.2165
91 5MF6 AR6 0.04891 0.40056 7.2165
92 5MF6 7M2 0.04891 0.40056 7.2165
93 5VCV 1N1 0.03453 0.40013 7.2165
94 3KRR DQX 0.01532 0.452 8.24742
95 4EUU BX7 0.007943 0.43661 8.24742
96 1PVN MZP 0.01656 0.43552 8.24742
97 1ZD9 GDP 0.01406 0.4157 8.24742
98 4LRJ ANP 0.01586 0.40936 8.24742
99 5UOX 8GY 0.02608 0.40381 8.24742
100 3HAV ATP 0.03554 0.40318 8.24742
101 4X7Q 3YR 0.02193 0.40308 8.24742
102 4IX4 ADP 0.02528 0.40273 8.24742
103 3AHW 2AM 0.0007909 0.47243 9.27835
104 5TO8 7FM 0.01355 0.4389 9.27835
105 3H9R TAK 0.003785 0.43113 9.27835
106 3W2E FAD 0.04319 0.41446 9.27835
107 3W2E NAD 0.04319 0.41446 9.27835
108 4WNP 3RJ 0.01669 0.40408 9.27835
109 5L0U 660 0.03744 0.40163 9.27835
110 2FV5 541 0.0446 0.40118 9.27835
111 1RNT 2GP 0.000001197 0.62686 10.3093
112 1FUT 2GP 0.0000006757 0.61007 10.3093
113 4DXJ 0M9 0.01775 0.42211 10.3093
114 4CLI 5P8 0.03206 0.41997 10.3093
115 2WTX VDO 0.03368 0.41549 10.3093
116 2WTX UDP 0.03234 0.41549 10.3093
117 4DXJ IPE 0.02741 0.41359 10.3093
118 4FMU 0UM 0.02372 0.40889 10.3093
119 2Y6O 1N1 0.02257 0.40651 10.3093
120 3KFL ME8 0.03104 0.40607 10.3093
121 4PJT 2YQ 0.04451 0.4025 10.3093
122 1LRW PQQ 0.02305 0.40568 10.8434
123 2Q7D ANP 0.006883 0.44085 11.3402
124 2PUL ACP 0.008492 0.42231 11.3402
125 4NW6 2NS 0.02635 0.41545 11.3402
126 4CRL C1I 0.03579 0.40898 11.3402
127 3LQV ADE 0.01539 0.40549 11.3402
128 5V22 SAH 0.02344 0.40436 11.3402
129 3S6X SIA GAL BGC 0.01726 0.40104 11.3402
130 5BV3 M7G 0.03007 0.40058 11.3402
131 2XG5 EC5 0.004862 0.42752 12.3711
132 2XG5 EC2 0.004862 0.42752 12.3711
133 3AKK ADP 0.01328 0.41623 12.3711
134 2JLD AG1 0.01403 0.43245 13.4021
135 3RWO GDP 0.01897 0.41638 13.4021
136 3FXU TSU 0.02163 0.41385 13.4021
137 4UCI SAM 0.02731 0.40121 13.4021
138 2XVD AS6 0.02273 0.4153 14.433
139 1S7G NAD 0.03746 0.40707 15.4639
140 2IO8 ADP 0.03127 0.40201 15.4639
141 3LDW IPE 0.02208 0.41584 16.4948
142 3WVR AMP 0.01257 0.41255 16.4948
143 1YNH SUO 0.02426 0.41096 16.4948
144 5ODQ FAD 0.01498 0.44167 17.5258
145 4E1Z 0MX 0.02182 0.40794 19.5876
146 5B2E MQG 0.02048 0.40318 19.5876
147 4CNK FAD 0.02402 0.42551 20.6186
148 5LXT ACP 0.02641 0.40581 20.6186
149 3LXK MI1 0.01719 0.41979 22.6804
150 1OPK P16 0.04609 0.40165 22.6804
151 5VC5 96M 0.008352 0.43839 23.7113
152 5COU ATP 0.02401 0.40008 26.8041
153 3KRL KRL 0.007731 0.43289 27.8351
154 1GOY 3GP 0.00000000003639 0.82072 28.866
155 5K2M ADP 0.02519 0.407 30.9278
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