Receptor
PDB id Resolution Class Description Source Keywords
4OI1 2.3 Å NON-ENZYME: OTHER CLP1 BOUND TO SSRNA DINUCLEOTIDE GC, ADP, ALF4-, AND MG2+(TR STATE, DATA SET II) CAENORHABDITIS ELEGANS POLYNUCLEOTIDE KINASE RNA BINDING PROTEIN-RNA COMPLEX
Ref.: RNA SPECIFICITY AND REGULATION OF CATALYSIS IN THE EUKARYOTIC POLYNUCLEOTIDE KINASE CLP1. MOL.CELL V. 54 975 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:502;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
2PE A:504;
Invalid;
none;
submit data
414.488 C18 H38 O10 C(COC...
ADP ALF A:501;
Valid;
none;
submit data
527.153 n/a P(=O)...
G C B:1;
Valid;
none;
submit data
587.419 n/a P(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4OHY 2 Å NON-ENZYME: OTHER C. ELEGANS CLP1 BOUND TO SSRNA DINUCLEOTIDE GC, AMP-PNP, AND MG2+(INHIBITED SUBSTRATE BOUND STATE) CAENORHABDITIS ELEGANS POLYNUCLEOTIDE KINASE RNA BINDING PROTEIN-RNA COMPLEX
Ref.: RNA SPECIFICITY AND REGULATION OF CATALYSIS IN THE EUKARYOTIC POLYNUCLEOTIDE KINASE CLP1. MOL.CELL V. 54 975 2014
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4OHZ - G A A A n/a n/a
2 4OI0 - ADP ALF n/a n/a
3 4OHW - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 4OHY - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
5 4OHV - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 4OI1 - ADP ALF n/a n/a
7 4OHX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4OHZ - G A A A n/a n/a
2 4OI0 - ADP ALF n/a n/a
3 4OHW - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 4OHY - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
5 4OHV - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 4OI1 - ADP ALF n/a n/a
7 4OHX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 4OHZ - G A A A n/a n/a
2 4OI0 - ADP ALF n/a n/a
3 4OHW - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 4OHY - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
5 4OHV - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 4OI1 - ADP ALF n/a n/a
7 4OHX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ADP ALF; Similar ligands found: 307
No: Ligand ECFP6 Tc MDL keys Tc
1 ALF ADP 1 1
2 ADP ALF 1 1
3 ADP PO3 0.8 0.918919
4 ADP VO4 0.752941 0.907895
5 VO4 ADP 0.752941 0.907895
6 AF3 ADP 3PG 0.707071 0.961039
7 ADP BMA 0.703297 0.871795
8 GAP 0.697674 0.871795
9 AMP 0.683544 0.868421
10 A 0.683544 0.868421
11 A2D 0.679012 0.87013
12 ADP 0.674699 0.87013
13 ATP A A A 0.666667 0.906667
14 BA3 0.662651 0.87013
15 ABM 0.658537 0.846154
16 B4P 0.654762 0.87013
17 AP5 0.654762 0.87013
18 AT4 0.647059 0.8375
19 AN2 0.647059 0.858974
20 AP2 0.642857 0.8375
21 A12 0.642857 0.8375
22 DAL AMP 0.641304 0.883117
23 AR6 AR6 0.64 0.894737
24 M33 0.639535 0.858974
25 SRA 0.634146 0.825
26 HEJ 0.632184 0.87013
27 ACP 0.632184 0.848101
28 ATP 0.632184 0.87013
29 AHZ 0.627451 0.8
30 AQP 0.625 0.87013
31 APC 0.625 0.8375
32 APR 0.625 0.87013
33 5FA 0.625 0.87013
34 AR6 0.625 0.87013
35 ADX 0.62069 0.788235
36 CA0 0.62069 0.848101
37 AU1 0.62069 0.848101
38 AGS 0.617977 0.82716
39 AD9 0.617977 0.871795
40 SAP 0.617977 0.82716
41 50T 0.613636 0.858974
42 MYR AMP 0.612245 0.8
43 ATF 0.608696 0.909091
44 A A 0.608247 0.87013
45 PRX 0.606742 0.825
46 ANP 0.604396 0.848101
47 TAT 0.604396 0.8375
48 T99 0.604396 0.8375
49 ACQ 0.604396 0.848101
50 ADV 0.6 0.8375
51 RBY 0.6 0.8375
52 AMP DBH 0.588235 0.848101
53 4TA 0.585586 0.790698
54 6YZ 0.585106 0.848101
55 LMS 0.583333 0.767442
56 5AL 0.580645 0.858974
57 A1R 0.57732 0.817073
58 SON 0.573034 0.8375
59 MAP 0.572917 0.85
60 A22 0.572917 0.858974
61 TYR AMP 0.572816 0.85
62 AMP NAD 0.571429 0.883117
63 AOC 0.569767 0.779221
64 SRP 0.568421 0.8375
65 5SV 0.56701 0.785714
66 PO4 PO4 A A A A PO4 0.565657 0.88
67 ALF GDP 0.565657 0.9125
68 GDP ALF 0.565657 0.9125
69 9X8 0.565657 0.82716
70 ARG AMP 0.561905 0.790698
71 ADQ 0.561224 0.848101
72 A3R 0.561224 0.817073
73 NAJ PZO 0.556522 0.829268
74 Z5A 0.554622 0.764045
75 BIS 0.554455 0.886076
76 ADN 0.551282 0.776316
77 RAB 0.551282 0.776316
78 XYA 0.551282 0.776316
79 OOB 0.55102 0.858974
80 25A 0.55102 0.87013
81 8QN 0.55102 0.858974
82 9ZD 0.55102 0.817073
83 9ZA 0.55102 0.817073
84 OAD 0.55 0.848101
85 AFH 0.54717 0.864198
86 LPA AMP 0.546296 0.8
87 PAJ 0.545455 0.797619
88 AMO 0.545455 0.8375
89 4AD 0.545455 0.85
90 5AS 0.544444 0.725275
91 NAD 0.54386 0.883117
92 9SN 0.543689 0.875
93 00A 0.54 0.8625
94 AHX 0.54 0.807229
95 DLL 0.54 0.858974
96 3OD 0.539216 0.848101
97 1ZZ 0.539216 0.77907
98 TXA 0.539216 0.8375
99 JB6 0.539216 0.817073
100 NAJ PYZ 0.537815 0.833333
101 5N5 0.5375 0.753247
102 3UK 0.534653 0.848101
103 A3D 0.534483 0.871795
104 25L 0.533981 0.858974
105 5CD 0.530864 0.786667
106 A4D 0.530864 0.753247
107 LAD 0.529412 0.797619
108 NAE 0.529412 0.85
109 PR8 0.529412 0.788235
110 WAQ 0.529412 0.817073
111 B5V 0.529412 0.8375
112 FYA 0.524272 0.835443
113 ME8 0.524272 0.77907
114 PTJ 0.524272 0.807229
115 NB8 0.524272 0.807229
116 NAQ 0.512397 0.829268
117 EP4 0.511905 0.716049
118 G5A 0.510417 0.725275
119 B5Y 0.509434 0.82716
120 B5M 0.509434 0.82716
121 YAP 0.509434 0.82716
122 FA5 0.509434 0.8375
123 G3A 0.509259 0.807229
124 ZID 0.508197 0.871795
125 DTA 0.505882 0.746835
126 M2T 0.505882 0.719512
127 3DH 0.505747 0.734177
128 XAH 0.504673 0.77907
129 GA7 0.504587 0.814815
130 G5P 0.504587 0.807229
131 G A A A 0.504274 0.829268
132 DQV 0.5 0.858974
133 GTA 0.5 0.8
134 MTA 0.5 0.734177
135 A3P 0.5 0.868421
136 4UV 0.5 0.82716
137 DND 0.5 0.860759
138 PAP 0.5 0.857143
139 NAI 0.5 0.817073
140 NXX 0.5 0.860759
141 OMR 0.495575 0.770115
142 TXE 0.495575 0.817073
143 TSB 0.49505 0.741573
144 A5A 0.494949 0.75
145 7D5 0.494253 0.7875
146 U A 0.491667 0.839506
147 A G 0.491525 0.839506
148 AP0 0.491228 0.807229
149 48N 0.491071 0.807229
150 7MD 0.490909 0.77907
151 4UU 0.490909 0.82716
152 SSA 0.49 0.725275
153 2A5 0.489583 0.802469
154 7D3 0.48913 0.790123
155 6RE 0.488889 0.722892
156 U A G G 0.487395 0.839506
157 UP5 0.486726 0.82716
158 NAX 0.486726 0.788235
159 TXD 0.486726 0.817073
160 6V0 0.486726 0.807229
161 TAD 0.486486 0.797619
162 54H 0.485149 0.733333
163 52H 0.485149 0.725275
164 VMS 0.485149 0.733333
165 ATR 0.484536 0.844156
166 NDE 0.484375 0.860759
167 A2P 0.483871 0.855263
168 3AM 0.483146 0.831169
169 TYM 0.482456 0.8375
170 LAQ 0.482143 0.77907
171 9K8 0.481132 0.758242
172 5CA 0.480392 0.725275
173 8X1 0.480392 0.702128
174 53H 0.480392 0.725275
175 N01 0.479339 0.883117
176 NMN AMP PO4 0.478992 0.85
177 139 0.478632 0.788235
178 T5A 0.478632 0.761364
179 4TC 0.478261 0.807229
180 J7C 0.478261 0.710843
181 A3N 0.478261 0.725
182 YLP 0.477876 0.761364
183 ZAS 0.477778 0.75
184 NDC 0.476923 0.829268
185 A A A 0.47619 0.883117
186 ALF 5GP 0.475248 0.9125
187 A4P 0.474138 0.744444
188 4UW 0.473684 0.797619
189 GJV 0.473118 0.714286
190 S4M 0.473118 0.655556
191 GSU 0.471698 0.725275
192 ENQ 0.471698 0.868421
193 P5A 0.471698 0.694737
194 DSZ 0.471154 0.725275
195 LSS 0.471154 0.709677
196 NSS 0.471154 0.744444
197 F2R 0.470588 0.761364
198 7D4 0.46875 0.790123
199 MAO 0.468085 0.704545
200 DSH 0.467391 0.690476
201 COD 0.466667 0.736264
202 NVA LMS 0.466667 0.72043
203 ADJ 0.466102 0.770115
204 UPA 0.465517 0.817073
205 YLB 0.465517 0.761364
206 YLC 0.465517 0.77907
207 7MC 0.465517 0.761364
208 5X8 0.463918 0.725
209 IMO 0.462366 0.831169
210 LEU LMS 0.462264 0.72043
211 CNA 0.462185 0.860759
212 A U 0.461538 0.85
213 V3L 0.46 0.87013
214 KAA 0.457944 0.702128
215 IOT 0.457627 0.752809
216 A2R 0.456311 0.858974
217 2AM 0.455556 0.820513
218 PPS 0.455446 0.767442
219 8PZ 0.454545 0.725275
220 CNV FAD 0.453901 0.764045
221 YLA 0.453782 0.761364
222 ITT 0.453608 0.820513
223 5AD 0.451219 0.706667
224 AV2 0.45098 0.822785
225 FAD NBT 0.450704 0.701031
226 YSA 0.45045 0.725275
227 SAH 0.45 0.707317
228 HFD 0.45 0.897436
229 AYB 0.45 0.752809
230 SFG 0.44898 0.7125
231 GDP AF3 0.448598 0.9125
232 FAD CNX 0.448276 0.68
233 M24 0.448 0.853659
234 4YB 0.447368 0.709677
235 80F 0.447154 0.761364
236 Y3J 0.447059 0.756757
237 7D7 0.445783 0.705128
238 SAM 0.445545 0.678161
239 PAX 0.445312 0.770115
240 P33 FDA 0.445205 0.715789
241 P6G FDA 0.445205 0.73913
242 A7D 0.443299 0.7375
243 BTX 0.442623 0.761364
244 6AD 0.441176 0.797619
245 OVE 0.44086 0.790123
246 SA8 0.44 0.674419
247 BT5 0.439024 0.752809
248 DZD 0.439024 0.797619
249 MHZ 0.438776 0.648352
250 71V 0.4375 0.795181
251 A3G 0.43617 0.7375
252 6C6 0.435644 0.792683
253 SAI 0.435644 0.719512
254 DAT 0.434343 0.790123
255 SMM 0.432692 0.674157
256 WSA 0.432203 0.733333
257 A C A C 0.432 0.829268
258 7C5 0.429825 0.756098
259 EEM 0.427184 0.697674
260 AAT 0.427184 0.674419
261 NAP 0.426357 0.871795
262 NAJ 0.42623 0.883117
263 A5D 0.425743 0.746835
264 YLY 0.425197 0.752809
265 PGS 0.424242 0.795181
266 TAP 0.423077 0.839506
267 NA7 0.422018 0.8375
268 D5M 0.421053 0.7875
269 DA 0.421053 0.7875
270 NEC 0.421053 0.6875
271 U A C C 0.420635 0.839506
272 GEK 0.420561 0.722892
273 AVV 0.420561 0.875
274 649 0.420168 0.694737
275 NA0 0.419847 0.860759
276 EAD 0.419847 0.788235
277 NHD 0.419355 0.858974
278 NIA 0.419355 0.761905
279 S7M 0.419048 0.678161
280 P1H 0.41791 0.770115
281 6IA 0.417476 0.755814
282 3AT 0.417476 0.846154
283 DTP 0.417476 0.790123
284 FAD NBA 0.415584 0.68
285 N0B 0.415385 0.761364
286 A3S 0.414141 0.746835
287 C2R 0.413043 0.7875
288 AMZ 0.413043 0.797468
289 ARU 0.412844 0.797619
290 NFD 0.412698 0.910256
291 GGZ 0.411215 0.744186
292 101 0.410526 0.7875
293 2SA 0.409524 0.814815
294 K15 0.409091 0.651685
295 U A A U 0.409091 0.839506
296 A6D 0.409091 0.709302
297 6K6 0.407407 0.833333
298 A3T 0.405941 0.75641
299 8Q2 0.404959 0.702128
300 AIR 0.404494 0.805195
301 0UM 0.40367 0.666667
302 6FA 0.402878 0.761364
303 AAM 0.402062 0.868421
304 FB0 0.40146 0.712766
305 7DD 0.4 0.857143
306 ACK 0.4 0.792208
307 62X 0.4 0.637363
Ligand no: 2; Ligand: G C ; Similar ligands found: 114
No: Ligand ECFP6 Tc MDL keys Tc
1 G C 1 1
2 G G G C 0.857143 0.9625
3 A G C C 0.849558 0.987179
4 G C C C 0.820513 0.974684
5 G U 0.801802 1
6 G G G RPC 0.756522 0.949367
7 A G U 0.694656 0.987342
8 GPC 0.680328 0.927711
9 A G U U 0.669118 0.987342
10 A C A C 0.634921 0.949367
11 CG2 0.634146 0.9625
12 G G 0.62931 0.925
13 A U C C 0.626866 0.949367
14 G A A A 0.611111 0.949367
15 C C C C 0.609091 0.884615
16 U A C C 0.584615 0.936709
17 C C 0.581818 0.871795
18 G U34 0.574803 0.987342
19 A G 0.573643 0.936709
20 U A G G 0.569231 0.936709
21 3GP 0.566038 0.898734
22 G3D 0.561404 0.8875
23 A U 0.546875 0.924051
24 G4P 0.538462 0.8875
25 ALF 5GP 0.530435 0.869048
26 DC DG 0.530303 0.939024
27 GCP G 0.528926 0.898734
28 0O2 0.520661 0.8875
29 U2G 0.519084 0.9625
30 APC G U 0.514706 0.888889
31 G 0.513514 0.911392
32 5GP 0.513514 0.911392
33 GPG 0.508197 0.91358
34 GDP 0.504348 0.9
35 GDP AF3 0.504132 0.869048
36 ALF GDP 0.504132 0.869048
37 GDP ALF 0.504132 0.869048
38 DG DC 0.496454 0.903614
39 CSQ 0.491935 0.829268
40 CSV 0.491935 0.829268
41 GP2 0.491379 0.86747
42 U A A U 0.48951 0.9125
43 GNH 0.487179 0.888889
44 GSP 0.483333 0.857143
45 GP3 0.482759 0.901235
46 2GP 0.482143 0.8875
47 CDP 0.481818 0.8375
48 CAR 0.481132 0.848101
49 GMP 0.481132 0.835443
50 C 0.481132 0.848101
51 C5P 0.481132 0.848101
52 GTP 0.478992 0.9
53 GAV 0.47541 0.86747
54 GCP 0.475 0.878049
55 G2P 0.471074 0.86747
56 GDP 7MG 0.469231 0.91358
57 GDC 0.46875 0.91358
58 GKE 0.46875 0.91358
59 GDD 0.46875 0.91358
60 CGP 0.467153 0.915663
61 GMV 0.466667 0.878049
62 7XL 0.465517 0.817073
63 G1R 0.46281 0.888889
64 9GM 0.459016 0.878049
65 GNP 0.459016 0.878049
66 HF4 0.45614 0.8375
67 CTP 0.45614 0.8375
68 C5G 0.455285 0.839506
69 DC DG DA DC 0.454545 0.903614
70 UCG 0.452055 0.9375
71 U A 0.450704 0.9125
72 DG DA DC DG 0.449367 0.927711
73 CDM 0.447154 0.77907
74 DA DC DG DA 0.444444 0.892857
75 JB2 0.443609 0.890244
76 91P 0.442029 0.939024
77 G2R 0.440945 0.86747
78 DC DG DT DA 0.440476 0.883721
79 CDC 0.439024 0.744444
80 U U 0.439024 0.822785
81 DG DG 0.4375 0.891566
82 TPG 0.435374 0.824176
83 Y9Z 0.435115 0.83908
84 DT DA DC DG 0.434524 0.883721
85 GKD 0.432836 0.91358
86 GDR 0.431818 0.890244
87 GFB 0.431818 0.890244
88 C2G 0.429752 0.82716
89 CTP C C C C 0.42963 0.858974
90 6CK 0.428571 0.869048
91 G3A 0.428571 0.901235
92 YGP 0.427481 0.903614
93 CTN 0.427184 0.759494
94 AR3 0.427184 0.759494
95 G1R G1R 0.425676 0.902439
96 G5P 0.425373 0.901235
97 NGD 0.421429 0.91358
98 BGO 0.421429 0.857143
99 GTG 0.421053 0.891566
100 GDX 0.419118 0.901235
101 GPD 0.419118 0.858824
102 ZGP 0.41844 0.829545
103 3PD UM3 0.41844 0.938272
104 C3P 0.418182 0.835443
105 CXY 0.417323 0.817073
106 P1G 0.416667 0.829268
107 JB3 0.414286 0.879518
108 CAG 0.413793 0.840909
109 PGD O 0.413333 0.853933
110 FEG 0.411348 0.83908
111 2AA 0.405594 0.682692
112 GPX 0.403101 0.851852
113 2MD 0.402778 0.872093
114 P2G 0.4 0.839506
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4OHY; Ligand: ANP; 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: 4ohy.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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