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Receptor
PDB id Resolution Class Description Source Keywords
2PNZ 2.14 Å EC: 3.1.13.- CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED WITH UDP AND GMP PYROCOCCUS ABYSSI RNASE PH HYDROLASE/HYDROLASE COMPLEX
Ref.: INSIGHTS INTO THE MECHANISM OF PROGRESSIVE RNA DEGRADATION BY THE ARCHAEAL EXOSOME. J.BIOL.CHEM. V. 283 14120 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP A:279;
Valid;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
MPD A:251;
A:252;
A:282;
B:280;
B:281;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
118.174 C6 H14 O2 C[C@@...
UDP A:250;
Valid;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PNZ 2.14 Å EC: 3.1.13.- CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED WITH UDP AND GMP PYROCOCCUS ABYSSI RNASE PH HYDROLASE/HYDROLASE COMPLEX
Ref.: INSIGHTS INTO THE MECHANISM OF PROGRESSIVE RNA DEGRADATION BY THE ARCHAEAL EXOSOME. J.BIOL.CHEM. V. 283 14120 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2PO2 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2PNZ - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2PO2 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2PNZ - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2PO2 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2PNZ - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP; Similar ligands found: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 G 1 1
2 5GP 1 1
3 GDP 0.828947 0.986486
4 GP3 0.815789 0.960526
5 GP2 0.805195 0.948052
6 GTP 0.797468 0.986486
7 GNH 0.794872 0.973333
8 G2P 0.777778 0.948052
9 GMV 0.775 0.960526
10 G1R 0.765432 0.973333
11 GCP 0.765432 0.960526
12 GAV 0.759036 0.948052
13 GSP 0.756098 0.935897
14 GNP 0.756098 0.960526
15 9GM 0.756098 0.960526
16 ALF 5GP 0.753086 0.9
17 GMP 0.732394 0.866667
18 GPG 0.724138 0.948052
19 G2R 0.712644 0.948052
20 ALF GDP 0.701149 0.9
21 GDP ALF 0.701149 0.9
22 GDP AF3 0.701149 0.9
23 GKE 0.692308 0.948052
24 Y9Z 0.692308 0.890244
25 GDC 0.692308 0.948052
26 GDD 0.692308 0.948052
27 YGP 0.681319 0.9125
28 G3A 0.677419 0.960526
29 G5P 0.670213 0.960526
30 GFB 0.666667 0.948052
31 GDR 0.666667 0.948052
32 GTG 0.666667 0.924051
33 6CK 0.659574 0.924051
34 3GP 0.65 0.959459
35 G G 0.648936 0.960526
36 GKD 0.645833 0.948052
37 JB2 0.645833 0.948052
38 GDX 0.639175 0.960526
39 GPD 0.639175 0.9125
40 GDP 7MG 0.635417 0.923077
41 G3D 0.617977 0.972973
42 U2G 0.617647 0.924051
43 2GP 0.609756 0.946667
44 IMP 0.609756 0.972603
45 JB3 0.607843 0.935897
46 CG2 0.605769 0.924051
47 G4P 0.604396 0.972973
48 DGP 0.60241 0.922078
49 DG 0.60241 0.922078
50 FEG 0.601942 0.890244
51 NGD 0.601942 0.948052
52 ZGP 0.596154 0.879518
53 0O2 0.595745 0.972973
54 2MD 0.584906 0.879518
55 G7M 0.583333 0.960526
56 CAG 0.583333 0.869048
57 G A A A 0.579439 0.935065
58 A G 0.579439 0.947368
59 U A G G 0.574074 0.947368
60 MGD 0.568807 0.879518
61 DBG 0.566372 0.935897
62 PGD 0.5625 0.9125
63 MD1 0.5625 0.879518
64 P2G 0.55814 0.894737
65 GCP G 0.556701 0.933333
66 FE9 0.553571 0.784946
67 P1G 0.545455 0.883117
68 GH3 0.542553 0.96
69 TPG 0.53913 0.829545
70 GPX 0.53125 0.933333
71 DGI 0.527473 0.910256
72 G1R G1R 0.525862 0.911392
73 G U 0.522936 0.911392
74 PGD O 0.521368 0.83908
75 DGT 0.521277 0.910256
76 G4M 0.520325 0.869048
77 AKW 0.513761 0.878049
78 G C 0.513514 0.911392
79 93A 0.511364 0.821429
80 IDP 0.505495 0.959459
81 MGQ 0.505155 0.948052
82 C2R 0.5 0.893333
83 A 0.5 0.905405
84 AMZ 0.5 0.905405
85 BGO 0.5 0.911392
86 AMP 0.5 0.905405
87 AIR 0.493671 0.890411
88 MGV 0.49 0.901235
89 SGP 0.488889 0.8375
90 NIA 0.488095 0.8375
91 GPC 0.474138 0.890244
92 G G G RPC 0.473684 0.886076
93 GGM 0.473684 0.888889
94 71V 0.47191 0.85
95 APC G U 0.470085 0.897436
96 R5I 0.46875 0.933333
97 R7I 0.46875 0.933333
98 MGP 0.46875 0.948052
99 35G 0.468085 0.945946
100 PCG 0.468085 0.945946
101 C2E 0.468085 0.933333
102 G1G 0.466102 0.9125
103 AAM 0.465909 0.905405
104 RMB 0.465909 0.813333
105 FAI 0.465909 0.905405
106 7RA 0.465909 0.918919
107 1RB 0.465116 0.824324
108 6G0 0.463918 0.948052
109 5GP 5GP 0.463158 0.894737
110 G G G C 0.462185 0.924051
111 RBZ 0.45977 0.815789
112 UCG 0.459016 0.923077
113 A G C C 0.458333 0.923077
114 DG DG 0.456311 0.876543
115 G U34 0.45614 0.9
116 IMO 0.449438 0.866667
117 A G U 0.446154 0.9
118 G C C C 0.443548 0.935897
119 IRN 0.443038 0.808219
120 PMO 0.43956 0.792208
121 7RP 0.438202 0.864865
122 GTA 0.436364 0.924051
123 JLN 0.433333 0.88
124 P2P 0.433333 0.842105
125 A G U U 0.42963 0.9
126 XMP 0.428571 0.907895
127 PGS 0.425532 0.804878
128 RVP 0.423529 0.84
129 G2Q 0.423077 0.948052
130 ADP 0.419355 0.906667
131 ABM 0.417582 0.857143
132 A2D 0.417582 0.881579
133 PRT 0.416667 0.945946
134 GUO 0.415842 0.932432
135 AT4 0.414894 0.871795
136 CA0 0.410526 0.883117
137 2SA 0.41 0.871795
138 1YD 0.409091 0.933333
139 4BW 0.409091 0.933333
140 A12 0.408602 0.871795
141 AP2 0.408602 0.871795
142 BA3 0.408602 0.881579
143 6C6 0.408163 0.825
144 25A 0.407767 0.906667
145 NOS 0.406977 0.813333
146 HEJ 0.40625 0.906667
147 ATP 0.40625 0.906667
148 AP5 0.404255 0.881579
149 B4P 0.404255 0.881579
150 ACQ 0.40404 0.883117
151 6IA 0.40404 0.785714
152 ANP 0.40404 0.883117
153 CGP 0.403361 0.878049
154 APC 0.402062 0.871795
155 3ZE 0.402062 0.871795
156 5FA 0.402062 0.906667
157 AQP 0.402062 0.906667
158 N6P 0.4 0.853333
159 AN2 0.4 0.894737
Ligand no: 2; Ligand: UDP; Similar ligands found: 117
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 UNP 0.8 0.970149
4 U5P 0.78125 0.984615
5 U 0.78125 0.984615
6 UPU 0.72973 0.940298
7 2KH 0.722222 0.970149
8 44P 0.720588 0.955882
9 UFM 0.717949 0.941176
10 GDU 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GUD 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UPP 0.705128 0.941176
17 UDH 0.705128 0.864865
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UPF 0.691358 0.888889
21 UAD 0.670732 0.941176
22 UDX 0.670732 0.941176
23 3UC 0.658824 0.888889
24 USQ 0.654762 0.820513
25 UGB 0.654762 0.955224
26 UGA 0.654762 0.955224
27 G3N 0.647059 0.914286
28 UDM 0.636364 0.914286
29 URI 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 Y6W 0.607143 0.888889
33 CDP 0.605263 0.942029
34 HP7 0.591398 0.941176
35 UD7 0.591398 0.927536
36 MJZ 0.585106 0.914286
37 IUG 0.583333 0.810127
38 F5G 0.578947 0.927536
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 F5P 0.578947 0.914286
42 UD4 0.578947 0.914286
43 CJB 0.573529 0.820895
44 UDZ 0.571429 0.853333
45 DUD 0.571429 0.913043
46 UP5 0.571429 0.853333
47 U U 0.563218 0.955224
48 EPZ 0.56 0.914286
49 5GW 0.559524 0.942029
50 EPU 0.554455 0.901408
51 EEB 0.554455 0.901408
52 U3P 0.547945 0.939394
53 UA3 0.547945 0.939394
54 4TC 0.544554 0.831169
55 HF4 0.54321 0.942029
56 CTP 0.54321 0.942029
57 CSQ 0.531915 0.851351
58 CSV 0.531915 0.851351
59 DUT 0.52439 0.913043
60 4GW 0.516484 0.915493
61 UMA 0.513761 0.914286
62 U4S 0.513158 0.753425
63 U2P 0.506667 0.954545
64 U2S 0.5 0.767123
65 U3S 0.5 0.753425
66 PUP 0.48913 0.913043
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 U22 0.486957 0.790123
70 DKX 0.486486 0.746479
71 U1S 0.482759 0.75
72 A U 0.481132 0.805195
73 2QR 0.478632 0.822785
74 5FU 0.474359 0.914286
75 G U 0.472222 0.7875
76 8OD 0.47191 0.851351
77 C5G 0.468085 0.888889
78 7XL 0.465909 0.888889
79 U U U U 0.461538 0.940298
80 UMF 0.461538 0.857143
81 G8D 0.460674 0.855263
82 UTP U U U 0.456522 0.895522
83 2TU 0.452055 0.774648
84 4RA 0.451613 0.855263
85 C2G 0.450549 0.901408
86 DU 0.45 0.898551
87 UMP 0.45 0.898551
88 C 0.45 0.927536
89 CAR 0.45 0.927536
90 C5P 0.45 0.927536
91 UAG 0.448 0.864865
92 CDC 0.446809 0.777778
93 5BU 0.444444 0.914286
94 UD0 0.444444 0.844156
95 N3E 0.440476 0.733333
96 UC5 0.440476 0.9
97 UUA 0.438356 0.772727
98 DUP 0.431818 0.887324
99 2GW 0.431373 0.901408
100 M7G 0.430108 0.780488
101 CNU 0.428571 0.927536
102 CDM 0.427083 0.842105
103 H6Y 0.425532 0.851351
104 16B 0.421687 0.888889
105 S5P 0.419753 0.915493
106 8GT 0.419355 0.855263
107 CXY 0.418367 0.888889
108 UPA 0.418182 0.842105
109 U2G 0.410714 0.822785
110 U A A U 0.409836 0.842105
111 UML 0.408759 0.810127
112 UP6 0.407407 0.871429
113 M7M 0.40625 0.771084
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
117 PMP UD1 0.401575 0.7875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PNZ; Ligand: 5GP; Similar sites found with APoc: 64
This union binding pocket(no: 1) in the query (biounit: 2pnz.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 5GUD NDP 2.52708
2 4ONA UW1 2.81124
3 3Q60 ATP 2.81124
4 5USZ SKE 2.88809
5 1MUU GDX 3.2491
6 4UX9 ANP 3.61011
7 2BNF UTP 3.61011
8 3RO7 TDR 3.77358
9 1O5R FR9 3.97112
10 4AT3 LTI 3.97112
11 1BYG STU 3.97112
12 4A4X JUP 4.01606
13 5UY8 AMZ 4.01606
14 4WNP 3RJ 4.01606
15 3ZNN FAD 4.33213
16 3ZNN 4WL 4.33213
17 1U59 STU 4.33213
18 6EQS BV8 4.41767
19 3JQQ FAD 4.81928
20 3K87 FAD 4.86486
21 4UAL 3FV 5.22088
22 3KH5 ADP 5.41516
23 3KH5 AMP 5.41516
24 2O3Z AI7 5.53506
25 1KQF MGD 5.62249
26 3ZOK GLY 5.62249
27 5LLT DND 5.6338
28 3FCI 3FI 5.8296
29 1LBF 137 6.07287
30 1I9G SAM 6.4257
31 1EKO I84 6.4982
32 1EKO NAP 6.4982
33 3A1C ACP 6.82731
34 4K81 GTP 6.82731
35 4GKV NAD 7.22022
36 2Q4H AMP 7.58123
37 2PWY SAH 7.75194
38 5WNL STU 8.43373
39 5ZCT ANP 8.43373
40 4A1O JLN 8.83534
41 3E5A VX6 9.32836
42 3C6K MTA 9.38628
43 3C6K SPD 9.38628
44 1RC0 KT5 9.56938
45 5JGA 6KC 9.63855
46 5LI1 ANP 9.74729
47 2RIF AMP 9.92908
48 1Z4O GL1 9.95475
49 1I3U RR1 10.2362
50 4L2I NAD 10.8434
51 4L2I FAD 10.8434
52 5N87 N66 10.8626
53 4QRH 0O2 11.9048
54 5NKN LOC 12.069
55 2C3H GLC GLC 12.2449
56 2VHJ ADP 12.6888
57 4Y8D 49J 13.5714
58 1ZC3 GNP 16.8142
59 4DPL NAP 16.8675
60 2H21 SAM 19.2771
61 2X2M X2M 19.8556
62 1O94 AMP 21.6867
63 1O97 FAD 21.6867
64 1O97 AMP 21.6867
Pocket No.: 2; Query (leader) PDB : 2PNZ; Ligand: 5GP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2pnz.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2PNZ; Ligand: 5GP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2pnz.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2PNZ; Ligand: UDP; Similar sites found with APoc: 16
This union binding pocket(no: 4) in the query (biounit: 2pnz.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4FHD 0TT 2.52708
2 4FHD EEM 2.52708
3 6AYU F6P 3.61446
4 4WW8 VD9 4.41767
5 6F7L FAD 5.22088
6 1E5F PLP 5.77617
7 4IOK ADP 6.13718
8 6AM8 PLT 6.4982
9 3WD1 ST7 8.30325
10 2O66 FLC 8.88889
11 1ESM COA 9.23695
12 5UWA 8ND 9.35961
13 2OG2 MLI 9.38628
14 5X2Z 3LM 10.4693
15 3RV5 DXC 11.236
16 4OX5 DAL 14.9733
Pocket No.: 5; Query (leader) PDB : 2PNZ; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2pnz.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2PNZ; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2pnz.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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