Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2GP B:98;
Valid;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
BGC A:99;
Invalid;
none;
submit data
180.156 C6 H12 O6 C([C@...
SO4 A:98;
B:100;
C:198;
Invalid;
Invalid;
Invalid;
none;
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: 2GP; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 2GP 1 1
2 3GP 0.733333 0.959459
3 GPG 0.701149 0.948052
4 GMP 0.657534 0.866667
5 G3D 0.613636 0.972973
6 G 0.609756 0.946667
7 5GP 0.609756 0.946667
8 P2G 0.590361 0.92
9 GSP 0.577778 0.911392
10 GDP 0.574713 0.96
11 GNH 0.568182 0.947368
12 G4P 0.565217 0.972973
13 GP3 0.563218 0.935065
14 P1G 0.55814 0.907895
15 GP2 0.556818 0.923077
16 GTP 0.555556 0.96
17 G2P 0.543478 0.923077
18 0O2 0.541667 0.972973
19 GMV 0.538462 0.935065
20 GDC 0.535354 0.948052
21 GKE 0.535354 0.948052
22 GDD 0.535354 0.948052
23 G1R 0.532609 0.947368
24 GCP 0.532609 0.935065
25 GAV 0.531915 0.923077
26 GDP MG 0.527473 0.886076
27 GNP 0.526882 0.935065
28 ALF 5GP 0.521739 0.853659
29 GDP BEF 0.521739 0.864198
30 SGP 0.517241 0.860759
31 CG2 0.513761 0.924051
32 U2G 0.509259 0.924051
33 DGP 0.505747 0.922078
34 DG 0.505747 0.922078
35 GTP MG 0.505263 0.886076
36 GH3 0.505263 0.96
37 BEF GDP 0.505263 0.853659
38 G G 0.50505 0.897436
39 G2R 0.5 0.923077
40 GCP G 0.5 0.897436
41 GKD 0.5 0.948052
42 GPX 0.494845 0.959459
43 GDP ALF 0.489796 0.853659
44 GDP AF3 0.489796 0.853659
45 DGI 0.48913 0.935065
46 2AM 0.487805 0.905405
47 GFB 0.485437 0.923077
48 GDR 0.485437 0.923077
49 GPC 0.482456 0.86747
50 G C 0.482143 0.8875
51 6CK 0.480769 0.9
52 G3A 0.480769 0.935065
53 YGP 0.480392 0.865854
54 G U34 0.477477 0.876543
55 G5P 0.47619 0.935065
56 Y9Z 0.475728 0.890244
57 G G U 0.471698 0.922078
58 JB2 0.471698 0.923077
59 GTG 0.471154 0.9
60 DGT 0.46875 0.935065
61 GDX 0.46729 0.935065
62 GPD 0.46729 0.888889
63 JB3 0.459459 0.911392
64 G G G RPC 0.45614 0.8625
65 BGO 0.455357 0.911392
66 G A A A 0.452174 0.910256
67 DG DG 0.45098 0.876543
68 G1G 0.449153 0.888889
69 GDP 7MG 0.448598 0.875
70 35G 0.446809 0.92
71 C2E 0.446809 0.907895
72 PCG 0.446809 0.92
73 FEG 0.442478 0.845238
74 5GP 5GP 0.442105 0.87013
75 ZGP 0.438596 0.835294
76 U A G G 0.435897 0.897436
77 G G G C 0.433333 0.876543
78 2MD 0.431034 0.857143
79 GGM 0.431034 0.888889
80 UCG 0.430894 0.898734
81 NGD 0.429825 0.923077
82 A G C C 0.429752 0.875
83 APC G U 0.428571 0.873418
84 TPG 0.422764 0.808989
85 OVE 0.420455 0.87013
86 CAG 0.420168 0.847059
87 G C C C 0.416 0.8875
88 3ZE 0.410526 0.848101
89 MGD 0.408333 0.857143
90 PGD 0.406504 0.888889
91 4BW 0.40367 0.907895
92 1YD 0.40367 0.907895
93 OMC OMU OMG OMG U 0.402985 0.833333
94 A2P 0.402174 0.891892
95 DBG 0.4 0.911392
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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