Receptor
PDB id Resolution Class Description Source Keywords
5ark 2.28 Å EC: 3.1.27.- CRYSTAL STRUCTURE OF PORCINE RNASE 4 IN COMPLEX WITH DUMP SUS SCROFA RIBONUCLEASE 4 HYDROLASE RNA DEGRADATION
Ref.: STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY IN PORCIN 4. FEBS J. V. 283 912 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UMP B:1120;
C:1120;
A:1120;
D:1120;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
308.182 C9 H13 N2 O8 P C1[C@...
PO4 A:1121;
B:1121;
 Invalid;
Invalid;
 none;
none;
 submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ARK 2.28 Å EC: 3.1.27.- CRYSTAL STRUCTURE OF PORCINE RNASE 4 IN COMPLEX WITH DUMP SUS SCROFA RIBONUCLEASE 4 HYDROLASE RNA DEGRADATION
Ref.: STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY IN PORCIN 4. FEBS J. V. 283 912 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 5ARK - UMP C9 H13 N2 O8 P C1[C@@H]([....
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 5ARK - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 2RNF - UM3 C9 H13 N2 O8 P C1[C@@H]([....
50% Homology Family (83)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1Z6D Ki = 4.6 mM IMP C10 H13 N4 O8 P c1nc2c(n1[....
2 1O0H Ki = 1.2 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 1JVU - C2P C9 H14 N3 O8 P C1=CN(C(=O....
4 3D7B Ki = 203 uM U4S C13 H19 N3 O5 C1CCN(C1)C....
5 3FL1 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
6 6PVW Ki = 0.48 uM OZV C10 H16 N5 O18 P5 c1nc(c2c(n....
7 3D6Q Ki = 172 uM U3S C14 H21 N3 O5 C1CCN(CC1)....
8 3JW1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
9 3EV6 - RSF C6 H10 O3 C1CO[C@H]2....
10 2W5I Ki = 0.86 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 3D8Y Ki = 396 uM T3S C15 H23 N3 O4 CC1=CN(C(=....
12 3D6O Ki = 77 uM U1S C17 H25 N3 O7 CCOC(=O)C1....
13 3LXO Kd = 15 uM T3P C10 H15 N2 O8 P CC1=CN(C(=....
14 1O0O Ki = 8 uM A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
15 1RPF - C3P C9 H14 N3 O8 P C1=CN(C(=O....
16 3D6P Ki = 179 uM U2S C13 H19 N3 O6 C1COCCN1C[....
17 4G8V Ki = 1.6 uM 0EY C12 H15 N5 O6 c1c(nnn1[C....
18 1RNC - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
19 4WYZ Kd = 50 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
20 1ROB - C2P C9 H14 N3 O8 P C1=CN(C(=O....
21 1W4Q Ki = 5.5 uM UMF C9 H12 F N2 O8 P C1=CN(C(=O....
22 6PVV Ki = 1.4 uM 5FA C10 H18 N5 O19 P5 c1nc(c2c(n....
23 1O0F Ki = 5 uM A3P C10 H15 N5 O10 P2 c1nc(c2c(n....
24 3EV4 - ETF C2 H3 F3 O C(C(F)(F)F....
25 1RCA - CGP C19 H25 N8 O10 P c1nc2c(n1[....
26 1RND - DGP C10 H14 N5 O7 P c1nc2c(n1[....
27 4RSK Kd = 47.4 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
28 1RCN - DA DT DA DA n/a n/a
29 6PVX Ki = 0.068 uM U5F C9 H17 N2 O21 P5 C1=CN(C(=O....
30 1RNM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
31 2W5K Ki = 12 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
32 2G8R Ki = 103 uM N3E C15 H21 N3 O7 C1CN(CCC1C....
33 1U1B Kd = 16 nM PAX C20 H27 N7 O20 P4 CC1=CN(C(=....
34 1QHC Ki = 27 nM PUA C19 H27 N7 O20 P4 c1nc(c2c(n....
35 3FL0 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
36 4WYP Kd = 440 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
37 1O0M Ki = 7.1 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
38 2QCA - DGP C10 H14 N5 O7 P c1nc2c(n1[....
39 3EV5 - TMO C3 H9 N O C[N+](C)(C....
40 4S18 - 1PT C6 H14 N2 Pt C1CC[C@@H]....
41 1EOS - U2G C19 H24 N7 O13 P c1nc2c(n1[....
42 4RTE - CPT Cl2 H6 N2 Pt [NH3][Pt](....
43 6XHC - V2G C12 H17 N6 O8 P c1nc(c2c(n....
44 1W4O Ki = 3 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
45 1RNN - C5P C9 H14 N3 O8 P C1=CN(C(=O....
46 2XOG Ki = 0.37 mM SFB C20 H28 N8 O11 S c1nc(c2c(n....
47 6YO1 - UVC C9 H12 N2 O9 V C1=CN(C(=O....
48 1W4P Ki = 18 uM UM3 C9 H13 N2 O8 P C1[C@@H]([....
49 1AFL Ki = 520 nM ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
50 3EV3 - TBU C4 H10 O CC(C)(C)O
51 3RID - CGP C19 H25 N8 O10 P c1nc2c(n1[....
52 1RPG - CPA C19 H25 N8 O9 P c1nc(c2c(n....
53 1WBU - WBU C4 H5 N3 O2 C1=C(C(=O)....
54 6QE9 - J9H C17 H18 N3 Pt Cc1ccc2ccc....
55 4G8Y Ki = 25.8 uM 0FT C13 H17 N5 O6 CC1=CN(C(=....
56 1JN4 Ki = 11.3 uM 139 C19 H25 N7 O14 P2 c1nc(c2c(n....
57 1O0N Ki = 82 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
58 1AFK Ki = 240 nM PAP C10 H16 N5 O13 P3 c1nc(c2c(n....
59 2XOI Ki = 0.00046 M SFB C20 H28 N8 O11 S c1nc(c2c(n....
60 1EOW - U2G C19 H24 N7 O13 P c1nc2c(n1[....
61 5OGH - C3P C9 H14 N3 O8 P C1=CN(C(=O....
62 5NA9 - QPT C6 H12 N2 O4 Pt C1CC2(C1)C....
63 1F0V - DC DG n/a n/a
64 2W5L Ki = 63 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
65 1RUV - UVC C9 H12 N2 O9 V C1=CN(C(=O....
66 1Z6S Ki = 46 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
67 4G90 Ki = 30.8 uM 0G0 C12 H14 F N5 O6 c1c(nnn1[C....
68 6F60 - DVW C27 H31 N7 O5 Pt CC1=CC=C2C....
69 2W5G Ki = 0.86 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
70 3D8Z Ki = 423 uM TXS C14 H21 N3 O4 CC1=CN(C(=....
71 5JLG - RU Ru [Ru+3]
72 11BA - UPA C19 H24 N7 O12 P c1nc(c2c(n....
73 1TQ9 - CPA C19 H25 N8 O9 P c1nc(c2c(n....
74 3DJO Ki = 40.8 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
75 1N3Z - U3P C9 H13 N2 O9 P C1=CN(C(=O....
76 3DJV Ki = 27.9 uM C3P C9 H14 N3 O8 P C1=CN(C(=O....
77 1R5C - CPA C19 H25 N8 O9 P c1nc(c2c(n....
78 3DJQ Ki = 1046.4 uM UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
79 3DJP Ki = 63.2 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
80 3DJX Ki = 1557.9 uM C5P C9 H14 N3 O8 P C1=CN(C(=O....
81 11BG - U2G C19 H24 N7 O13 P c1nc2c(n1[....
82 5ARK - UMP C9 H13 N2 O8 P C1[C@@H]([....
83 2RNF - UM3 C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: UMP; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 UMP 1 1
2 DU 1 1
3 DUD 0.8 0.985075
4 UC5 0.772727 0.970588
5 DUT 0.753623 0.985075
6 DUN 0.75 0.956522
7 DUP 0.742857 0.956522
8 DUT MG 0.694444 0.955224
9 DUS 0.692308 0.853333
10 DUR 0.683333 0.852941
11 UMP AF3 PO4 0.675676 0.876712
12 DDN 0.632353 1
13 UFP 0.591549 0.929577
14 BRU 0.583333 0.929577
15 5HU 0.583333 0.942857
16 TMP 0.583333 0.956522
17 UM3 0.57971 0.955224
18 5IU 0.575342 0.929577
19 DC 0.561644 0.928571
20 DCM 0.561644 0.928571
21 BVP 0.531646 0.942857
22 DU DU DU DU BRU DU DU 0.53125 0.864865
23 U 0.527778 0.911765
24 U5P 0.527778 0.911765
25 DDU 0.523077 0.753623
26 UMC 0.520548 0.941176
27 QBT 0.493333 0.927536
28 DUA 0.487805 0.783784
29 DU3 0.487805 0.780822
30 5CM 0.481013 0.890411
31 DU4 0.47619 0.76
32 TYD 0.469136 0.942857
33 YYY 0.451219 0.915493
34 UDP 0.45 0.898551
35 TTP 0.447059 0.942857
36 8OG 0.435294 0.835443
37 U2P 0.434211 0.884058
38 U3P 0.434211 0.897059
39 UA3 0.434211 0.897059
40 UTP 0.433735 0.898551
41 44P 0.43038 0.914286
42 DCP 0.430233 0.915493
43 U5F 0.428571 0.898551
44 0KX 0.425287 0.890411
45 DUX 0.411765 0.756757
46 2KH 0.411765 0.873239
47 UMF 0.410256 0.84507
48 UPU 0.409091 0.871429
49 F6G 0.409091 0.876712
50 TTP MG 0.409091 0.914286
51 139 0.409091 0.8
52 URI 0.408451 0.771429
53 TBD 0.406977 0.90411
54 DU DU DU DU BRU DA DU 0.40625 0.771084
55 PUA 0.405172 0.833333
56 UNP 0.402299 0.873239
57 UAD 0.4 0.873239
58 PUP 0.4 0.955882
59 UDX 0.4 0.873239
Similar Ligands (3D)
Ligand no: 1; Ligand: UMP; Similar ligands found: 228
No: Ligand Similarity coefficient
1 O7E 0.9818
2 UP6 0.9811
3 CAR 0.9786
4 C5P 0.9776
5 H2U 0.9734
6 DOC 0.9731
7 FN5 0.9709
8 CH 0.9709
9 C 0.9709
10 BMP 0.9657
11 5FU 0.9654
12 PSU 0.9649
13 NUP 0.9639
14 FDM 0.9637
15 NYM 0.9607
16 9L3 0.9600
17 DI 0.9588
18 16B 0.9581
19 DA 0.9576
20 D5M 0.9575
21 5BU 0.9565
22 AS 0.9552
23 BMQ 0.9550
24 TKW 0.9540
25 D4M 0.9520
26 2DT 0.9518
27 U6M 0.9472
28 FNU 0.9456
29 PFU 0.9436
30 S5P 0.9389
31 AMP 0.9373
32 6MA 0.9373
33 NIA 0.9372
34 AMZ 0.9352
35 C2R 0.9339
36 U4S 0.9318
37 IMP 0.9317
38 JW5 0.9289
39 IRP 0.9280
40 AIR 0.9272
41 T3S 0.9262
42 6CN 0.9250
43 FMP 0.9226
44 CNU 0.9218
45 8BR 0.9207
46 8OP 0.9197
47 CDP 0.9193
48 6SY 0.9172
49 ATM 0.9158
50 U2S 0.9156
51 VIB 0.9154
52 NMN 0.9150
53 DGP 0.9149
54 DG 0.9149
55 5HM 0.9140
56 NCN 0.9130
57 7D5 0.9123
58 U1S 0.9118
59 U3S 0.9118
60 CC7 0.9117
61 GAR 0.9071
62 0RA 0.9063
63 103 0.9062
64 TXS 0.9056
65 2GE 0.9052
66 27M 0.9047
67 5QT 0.9046
68 MTE 0.9036
69 ZAS 0.9035
70 M2T 0.9033
71 5GP 0.9002
72 G 0.9002
73 71V 0.8999
74 AOC 0.8989
75 FT1 0.8985
76 XMP 0.8981
77 6AU 0.8980
78 6OG 0.8979
79 AZU 0.8977
80 N5O 0.8973
81 OMP 0.8973
82 IRN 0.8969
83 IGP 0.8969
84 3RC 0.8965
85 CMP 0.8957
86 T7O 0.8956
87 QTJ 0.8953
88 HDI 0.8952
89 IMU 0.8944
90 FX5 0.8942
91 UN3 0.8936
92 K4T 0.8926
93 VKE 0.8917
94 NEC 0.8912
95 A3N 0.8912
96 S0J 0.8894
97 8GM 0.8889
98 FT2 0.8886
99 2JP 0.8880
100 M8Q 0.8875
101 FAI 0.8859
102 43J 0.8854
103 2T4 0.8854
104 K8W 0.8849
105 90J 0.8849
106 PZB 0.8844
107 6PG 0.8843
108 GA6 0.8843
109 2OM 0.8826
110 9RK 0.8826
111 RP1 0.8826
112 DRM 0.8822
113 43F 0.8816
114 90G 0.8810
115 G3P IDM 0.8805
116 JVD 0.8804
117 6JD 0.8804
118 GG5 0.8801
119 0SX 0.8797
120 T3P 0.8797
121 43G 0.8796
122 QTK 0.8794
123 MTA 0.8790
124 MTI 0.8789
125 U55 0.8784
126 MTH 0.8783
127 SP1 0.8783
128 ML2 0.8775
129 34L 0.8773
130 PB2 0.8764
131 20P 0.8761
132 IWH 0.8750
133 TWB 0.8748
134 1CE 0.8747
135 IPJ 0.8746
136 QTV 0.8744
137 OAQ 0.8742
138 42M 0.8740
139 TDH 0.8738
140 S1D 0.8737
141 101 0.8735
142 JSX 0.8733
143 SNJ 0.8731
144 MTM 0.8731
145 22T 0.8728
146 HDU 0.8728
147 WDW 0.8726
148 KU1 0.8726
149 15I 0.8725
150 TCL 0.8725
151 L02 0.8724
152 QTD 0.8722
153 SIJ 0.8716
154 HMK 0.8715
155 N8M 0.8713
156 PCG 0.8712
157 S45 0.8711
158 O7M 0.8709
159 9W8 0.8706
160 BHF 0.8706
161 JON 0.8698
162 0QX 0.8693
163 9XZ 0.8689
164 VBC 0.8686
165 4BH 0.8682
166 UUL 0.8671
167 69W 0.8664
168 F91 0.8662
169 O8M 0.8659
170 1Q2 0.8654
171 6JJ 0.8652
172 DZJ 0.8650
173 97K 0.8649
174 AZZ 0.8647
175 W1G 0.8645
176 C5Q 0.8642
177 4X2 0.8639
178 9HK 0.8639
179 49K 0.8637
180 I5A 0.8635
181 BL6 0.8634
182 583 0.8634
183 5KN 0.8629
184 8RK 0.8629
185 IPL 0.8629
186 SYD 0.8628
187 EUB 0.8623
188 3N4 0.8621
189 SJR 0.8619
190 BIT 0.8618
191 Q7U 0.8616
192 FBP 0.8616
193 613 0.8615
194 GO1 0.8615
195 H3W 0.8613
196 122 0.8606
197 35G 0.8606
198 CTN 0.8605
199 58L 0.8604
200 I22 0.8603
201 F5A 0.8602
202 JHY 0.8601
203 0QR 0.8600
204 RF2 0.8599
205 HVE 0.8596
206 1ER 0.8589
207 62D 0.8584
208 DCZ 0.8582
209 UN9 0.8570
210 THP 0.8570
211 MBY 0.8569
212 D25 0.8567
213 CAP 0.8564
214 121 0.8559
215 WLL 0.8551
216 WDT 0.8550
217 Z3R 0.8548
218 35K 0.8546
219 5WS 0.8542
220 CLM 0.8535
221 AFP 0.8535
222 JP5 0.8535
223 H48 0.8533
224 13F 0.8532
225 RGK 0.8530
226 EFX 0.8518
227 TVC 0.8518
228 6QT 0.8507
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ARK; Ligand: UMP; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 5ark.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2BZZ AP5 37.3134
Pocket No.: 2; Query (leader) PDB : 5ARK; Ligand: UMP; 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: 5ark.bio4) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5ARK; Ligand: UMP; 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: 5ark.bio3) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5ARK; Ligand: UMP; 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: 5ark.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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