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 5 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 5 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 5 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 (2D)
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 GCP 0.765432 0.960526
11 G1R 0.765432 0.973333
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 GDP BEF 0.743902 0.947368
18 GTP MG 0.73494 0.972973
19 GMP 0.732394 0.866667
20 GPG 0.724138 0.948052
21 G2R 0.712644 0.948052
22 GDP ALF 0.701149 0.9
23 GDP AF3 0.701149 0.9
24 GKE 0.692308 0.948052
25 GDC 0.692308 0.948052
26 Y9Z 0.692308 0.890244
27 GDD 0.692308 0.948052
28 YGP 0.681319 0.9125
29 G3A 0.677419 0.960526
30 G5P 0.670213 0.960526
31 KB7 0.666667 0.8375
32 GFB 0.666667 0.948052
33 GDR 0.666667 0.948052
34 GTG 0.666667 0.924051
35 6CK 0.659574 0.924051
36 3GP 0.65 0.959459
37 JB2 0.645833 0.948052
38 GKD 0.645833 0.948052
39 GDX 0.639175 0.960526
40 GPD 0.639175 0.9125
41 GDP 7MG 0.635417 0.923077
42 G3D 0.617977 0.972973
43 U2G 0.617647 0.924051
44 KBD 0.612903 0.8375
45 2GP 0.609756 0.946667
46 IMP 0.609756 0.972603
47 JB3 0.607843 0.935897
48 CG2 0.605769 0.924051
49 G4P 0.604396 0.972973
50 DG 0.60241 0.922078
51 DGP 0.60241 0.922078
52 NGD 0.601942 0.948052
53 FEG 0.601942 0.890244
54 ZGP 0.596154 0.879518
55 0O2 0.595745 0.972973
56 KBJ 0.587629 0.807229
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 MGD 0.568807 0.879518
61 DBG 0.566372 0.935897
62 MD1 0.5625 0.879518
63 PGD 0.5625 0.9125
64 P2G 0.55814 0.894737
65 FE9 0.553571 0.784946
66 P1G 0.545455 0.883117
67 GH3 0.542553 0.96
68 I2C FE2 CMO CMO 0.539823 0.818182
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 PGD O 0.521368 0.83908
74 DGT 0.521277 0.910256
75 G4M 0.520325 0.869048
76 AKW 0.513761 0.878049
77 G C 0.513514 0.911392
78 93A 0.511364 0.821429
79 IDP 0.505495 0.959459
80 MGQ 0.505155 0.948052
81 C2R 0.5 0.893333
82 A 0.5 0.905405
83 BGO 0.5 0.911392
84 AMZ 0.5 0.905405
85 AMP 0.5 0.905405
86 AIR 0.493671 0.890411
87 MGV 0.49 0.901235
88 QBQ 0.489362 0.972973
89 SGP 0.488889 0.8375
90 NIA 0.488095 0.8375
91 GPC 0.474138 0.890244
92 GGM 0.473684 0.888889
93 71V 0.47191 0.85
94 R5I 0.46875 0.933333
95 MGP 0.46875 0.948052
96 R7I 0.46875 0.933333
97 C2E 0.468085 0.933333
98 PCG 0.468085 0.945946
99 35G 0.468085 0.945946
100 G1G 0.466102 0.9125
101 7RA 0.465909 0.918919
102 FAI 0.465909 0.905405
103 AAM 0.465909 0.905405
104 RMB 0.465909 0.813333
105 1RB 0.465116 0.824324
106 6G0 0.463918 0.948052
107 5GP 5GP 0.463158 0.894737
108 RBZ 0.45977 0.815789
109 UCG 0.459016 0.923077
110 APC G U 0.458333 0.897436
111 IMO 0.449438 0.866667
112 6MZ 0.444444 0.868421
113 IRN 0.443038 0.808219
114 PMO 0.43956 0.792208
115 7RP 0.438202 0.864865
116 NYZ 0.4375 0.923077
117 GTA 0.436364 0.924051
118 JLN 0.433333 0.88
119 P2P 0.433333 0.842105
120 CZF 0.43299 0.92
121 XMP 0.428571 0.907895
122 M7G A2M G 0.427586 0.818182
123 PGS 0.425532 0.804878
124 RVP 0.423529 0.84
125 G2Q 0.423077 0.948052
126 ADP 0.419355 0.906667
127 ABM 0.417582 0.857143
128 45A 0.417582 0.857143
129 A2D 0.417582 0.881579
130 PRT 0.416667 0.945946
131 GUO 0.415842 0.932432
132 AT4 0.414894 0.871795
133 AMP MG 0.411111 0.866667
134 CA0 0.410526 0.883117
135 2SA 0.41 0.871795
136 OK8 0.41 0.87013
137 1YD 0.409091 0.933333
138 4BW 0.409091 0.933333
139 BA3 0.408602 0.881579
140 AP2 0.408602 0.871795
141 A12 0.408602 0.871795
142 6C6 0.408163 0.825
143 25A 0.407767 0.906667
144 NOS 0.406977 0.813333
145 ATP 0.40625 0.906667
146 KG4 0.40625 0.883117
147 HEJ 0.40625 0.906667
148 B4P 0.404255 0.881579
149 AP5 0.404255 0.881579
150 6IA 0.40404 0.785714
151 ACQ 0.40404 0.883117
152 ANP 0.40404 0.883117
153 CGP 0.403361 0.878049
154 3ZE 0.402062 0.871795
155 5FA 0.402062 0.906667
156 APC 0.402062 0.871795
157 AQP 0.402062 0.906667
158 AN2 0.4 0.894737
159 N6P 0.4 0.853333
Ligand no: 2; Ligand: UDP; Similar ligands found: 123
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 U5F 0.878788 1
4 UNP 0.8 0.970149
5 U5P 0.78125 0.984615
6 U 0.78125 0.984615
7 UPU 0.72973 0.940298
8 2KH 0.722222 0.970149
9 44P 0.720588 0.955882
10 UFM 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GDU 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UDH 0.705128 0.864865
17 UPP 0.705128 0.941176
18 UFG 0.691358 0.888889
19 U2F 0.691358 0.888889
20 UPF 0.691358 0.888889
21 AWU 0.6875 0.941176
22 UAD 0.670732 0.941176
23 UDX 0.670732 0.941176
24 3UC 0.658824 0.888889
25 UGA 0.654762 0.955224
26 UGB 0.654762 0.955224
27 USQ 0.654762 0.820513
28 G3N 0.647059 0.914286
29 UGF 0.647059 0.901408
30 UDM 0.636364 0.914286
31 URI 0.625 0.863636
32 UD1 0.622222 0.927536
33 UD2 0.622222 0.927536
34 UDP GAL 0.611765 0.913043
35 Y6W 0.607143 0.888889
36 CDP 0.605263 0.942029
37 HP7 0.591398 0.941176
38 UD7 0.591398 0.927536
39 MJZ 0.585106 0.914286
40 IUG 0.583333 0.810127
41 HWU 0.578947 0.901408
42 UD4 0.578947 0.914286
43 12V 0.578947 0.901408
44 F5G 0.578947 0.927536
45 F5P 0.578947 0.914286
46 CJB 0.573529 0.820895
47 UDZ 0.571429 0.853333
48 DUD 0.571429 0.913043
49 UP5 0.571429 0.853333
50 EPZ 0.56 0.914286
51 5GW 0.559524 0.942029
52 EEB 0.554455 0.901408
53 EPU 0.554455 0.901408
54 UA3 0.547945 0.939394
55 U3P 0.547945 0.939394
56 4TC 0.544554 0.831169
57 HF4 0.54321 0.942029
58 CTP 0.54321 0.942029
59 BUP 0.536585 0.928571
60 CSV 0.531915 0.851351
61 CSQ 0.531915 0.851351
62 DUT 0.52439 0.913043
63 4GW 0.516484 0.915493
64 UMA 0.513761 0.914286
65 U4S 0.513158 0.753425
66 U2P 0.506667 0.954545
67 U3S 0.5 0.753425
68 U2S 0.5 0.767123
69 FZK 0.494253 0.777778
70 PUP 0.48913 0.913043
71 U21 0.486957 0.810127
72 U20 0.486957 0.810127
73 U22 0.486957 0.790123
74 DKX 0.486486 0.746479
75 U1S 0.482759 0.75
76 0RC 0.482759 0.864865
77 2QR 0.478632 0.822785
78 5FU 0.474359 0.914286
79 LSU 0.472527 0.738095
80 8OD 0.47191 0.851351
81 C5G 0.468085 0.888889
82 7XL 0.465909 0.888889
83 UMF 0.461538 0.857143
84 G8D 0.460674 0.855263
85 2TM 0.45977 0.902778
86 UTP U U U 0.456522 0.895522
87 YSU 0.453608 0.746988
88 2TU 0.452055 0.774648
89 4RA 0.451613 0.855263
90 C2G 0.450549 0.901408
91 DU 0.45 0.898551
92 CAR 0.45 0.927536
93 UMP 0.45 0.898551
94 C5P 0.45 0.927536
95 C 0.45 0.927536
96 UAG 0.448 0.864865
97 CDC 0.446809 0.777778
98 5BU 0.444444 0.914286
99 UD0 0.444444 0.844156
100 N3E 0.440476 0.733333
101 UC5 0.440476 0.9
102 UUA 0.438356 0.772727
103 DUP 0.431818 0.887324
104 2GW 0.431373 0.901408
105 M7G 0.430108 0.780488
106 CNU 0.428571 0.927536
107 CDM 0.427083 0.842105
108 H6Y 0.425532 0.851351
109 16B 0.421687 0.888889
110 S5P 0.419753 0.915493
111 8GT 0.419355 0.855263
112 CDP MG 0.418605 0.885714
113 CXY 0.418367 0.888889
114 UPA 0.418182 0.842105
115 U2G 0.410714 0.822785
116 UML 0.408759 0.810127
117 UP6 0.407407 0.871429
118 M7M 0.40625 0.771084
119 1GW 0.40367 0.864865
120 BMP 0.402439 0.970149
121 APU 0.401786 0.828947
122 PMP UD1 0.401575 0.7875
123 DUT MG 0.4 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: 5GP; Similar ligands found: 181
No: Ligand Similarity coefficient
1 IMU 0.9908
2 EO7 0.9905
3 IRP 0.9761
4 LMS 0.9705
5 6CG 0.9705
6 FMP 0.9702
7 8GM 0.9670
8 6OG 0.9662
9 8BR 0.9643
10 SRA 0.9642
11 D5M 0.9581
12 8OP 0.9576
13 DI 0.9557
14 DA 0.9551
15 CMP 0.9481
16 5HM 0.9474
17 6SW 0.9448
18 AS 0.9446
19 8OG 0.9444
20 AOC 0.9444
21 6MA 0.9412
22 ZAS 0.9407
23 5BU 0.9398
24 PFU 0.9366
25 NEC 0.9346
26 7CH 0.9345
27 3DH 0.9341
28 A3N 0.9335
29 FNU 0.9328
30 N5O 0.9319
31 CNU 0.9319
32 BRU 0.9319
33 5AS 0.9308
34 5CM 0.9294
35 NCN 0.9288
36 TMP 0.9283
37 NYM 0.9281
38 QBT 0.9281
39 6SZ 0.9279
40 TKW 0.9278
41 Z8B 0.9277
42 5FU 0.9270
43 UFP 0.9262
44 M2T 0.9253
45 NMN 0.9252
46 U5P 0.9224
47 MTA 0.9223
48 SP1 0.9219
49 7D5 0.9218
50 6SX 0.9214
51 6RE 0.9211
52 J7C 0.9211
53 5IU 0.9207
54 MZP 0.9174
55 4X2 0.9152
56 NWQ 0.9140
57 5HU 0.9140
58 9L3 0.9138
59 C 0.9123
60 2DT 0.9120
61 D4M 0.9119
62 BMQ 0.9115
63 BMP 0.9108
64 EP4 0.9107
65 MCF 0.9100
66 UP6 0.9063
67 RP1 0.9062
68 6J7 0.9056
69 BVP 0.9055
70 DSH 0.9040
71 C5P 0.9030
72 O8M 0.9029
73 PRX 0.9015
74 UMP 0.9002
75 DC 0.8991
76 GJV 0.8990
77 DCM 0.8989
78 DU 0.8989
79 U 0.8986
80 NWZ 0.8980
81 H2U 0.8974
82 3F5 0.8969
83 SSI 0.8968
84 MTE 0.8960
85 NUP 0.8946
86 UMC 0.8941
87 GDP MG 0.8932
88 T3S 0.8920
89 S5P 0.8919
90 ICR 0.8905
91 FN5 0.8895
92 CH 0.8895
93 581 0.8894
94 U6M 0.8893
95 PSU 0.8871
96 16B 0.8861
97 M7G 0.8859
98 O02 0.8851
99 2FA 0.8850
100 CAR 0.8849
101 O7E 0.8845
102 DDN 0.8844
103 G5A 0.8843
104 A8M 0.8839
105 ADP MG 0.8838
106 6CN 0.8830
107 DUS 0.8828
108 A3P 0.8826
109 OMP 0.8819
110 M33 0.8818
111 AD3 0.8816
112 ATM 0.8807
113 JW5 0.8806
114 43J 0.8797
115 T7O 0.8794
116 6AU 0.8793
117 GNG 0.8784
118 ADN 0.8778
119 N8M 0.8776
120 7DD 0.8775
121 U4S 0.8771
122 GAP 0.8768
123 6AD 0.8762
124 ADX 0.8760
125 A4D 0.8759
126 5CD 0.8759
127 1BJ 0.8754
128 A2P 0.8752
129 S4M 0.8752
130 43H 0.8741
131 IXF 0.8739
132 SON 0.8729
133 DOC 0.8728
134 FMC 0.8728
135 DBM 0.8718
136 5YA 0.8713
137 NOC 0.8713
138 ARJ 0.8713
139 NWW 0.8700
140 U2S 0.8699
141 FKJ 0.8695
142 IY5 0.8695
143 13A 0.8685
144 5N5 0.8683
145 AU1 0.8679
146 DAT 0.8677
147 Y3J 0.8666
148 CL9 0.8665
149 IMH 0.8665
150 CC2 0.8659
151 UA2 0.8658
152 MG7 0.8657
153 2OM 0.8656
154 U3S 0.8655
155 U1S 0.8655
156 100 0.8648
157 M7M 0.8647
158 ECZ 0.8641
159 2ZI 0.8639
160 5FD 0.8639
161 O7M 0.8636
162 PNJ 0.8629
163 TBN 0.8621
164 RFZ 0.8610
165 3AD 0.8609
166 GLC G6P 0.8606
167 IXE 0.8598
168 5CJ 0.8596
169 M0Y 0.8587
170 LRT 0.8587
171 DN8 0.8586
172 824 0.8575
173 0NH 0.8561
174 IYX 0.8555
175 A5A 0.8547
176 9W8 0.8546
177 TXS 0.8537
178 6SY 0.8537
179 2GE 0.8529
180 5ID 0.8524
181 3BH 0.8521
Ligand no: 2; Ligand: UDP; Similar ligands found: 55
No: Ligand Similarity coefficient
1 YYY 0.9739
2 TYD 0.9699
3 TBD 0.9623
4 GCQ 0.9509
5 ADP 0.9410
6 DUN 0.9317
7 D4D 0.9237
8 ADX 0.9224
9 AU1 0.9218
10 AP2 0.9215
11 SON 0.9211
12 GDP 0.9193
13 DAT 0.9189
14 IDP 0.9155
15 PRX 0.9148
16 ADP MG 0.9122
17 BEF ADP 0.9122
18 AN2 0.9115
19 A12 0.9102
20 M33 0.9098
21 CA0 0.9083
22 G5A 0.9077
23 CUU 0.9055
24 GAP 0.8984
25 DGI 0.8977
26 GNH 0.8961
27 FZQ 0.8919
28 7D3 0.8915
29 DAL AMP 0.8905
30 H2U 0.8888
31 CH 0.8874
32 AZD 0.8849
33 PSU 0.8815
34 CK7 0.8802
35 AMP 0.8793
36 FN5 0.8781
37 6AD 0.8757
38 A5A 0.8754
39 HQ5 0.8747
40 DCM 0.8724
41 8LH 0.8718
42 8GD 0.8708
43 ATY 0.8691
44 BMQ 0.8679
45 U6M 0.8672
46 NUP 0.8671
47 DC 0.8658
48 DCP 0.8657
49 TMP 0.8642
50 C8M 0.8633
51 TTP 0.8581
52 ATP 0.8570
53 DDN 0.8568
54 C2R 0.8549
55 D4T 0.8531
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2pnz.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2pnz.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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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