-->
Receptor
PDB id Resolution Class Description Source Keywords
2RDE 1.92 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VCA0042 COMPLEXED WITH C-DI-GMP VIBRIO CHOLERAE C-DI-GMP VIBRIO CHOLERAE VCA0042 STRUCTURAL GENOMICS PSIPROTEIN STRUCTURE INITIATIVE NORTHEAST STRUCTURAL GENOMICSCONSORTIUM NESG UNKNOWN FUNCTION
Ref.: THE STRUCTURAL BASIS OF CYCLIC DIGUANYLATE SIGNAL TRANSDUCTION BY PILZ DOMAINS. EMBO J. V. 26 5153 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C2E A:301;
B:301;
Valid;
Valid;
none;
none;
Kd = 97.1 nM
690.411 C20 H24 N10 O14 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2RDE 1.92 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VCA0042 COMPLEXED WITH C-DI-GMP VIBRIO CHOLERAE C-DI-GMP VIBRIO CHOLERAE VCA0042 STRUCTURAL GENOMICS PSIPROTEIN STRUCTURE INITIATIVE NORTHEAST STRUCTURAL GENOMICSCONSORTIUM NESG UNKNOWN FUNCTION
Ref.: THE STRUCTURAL BASIS OF CYCLIC DIGUANYLATE SIGNAL TRANSDUCTION BY PILZ DOMAINS. EMBO J. V. 26 5153 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 2RDE Kd = 97.1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
2 2RDE Kd = 97.1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
2 2RDE Kd = 97.1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C2E; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 35G 1 0.986111
2 C2E 1 1
3 PCG 1 0.986111
4 4BW 0.806818 1
5 1YD 0.806818 1
6 5GP 5GP 0.743902 0.958904
7 4UR 0.731959 1
8 6SW 0.627907 0.944444
9 1YC 0.616162 0.972222
10 6J7 0.58427 0.934211
11 CMP 0.534091 0.902778
12 2BA 0.534091 0.916667
13 GMP 0.53012 0.828947
14 1SY 0.495575 1
15 SGP 0.483871 0.825
16 6SZ 0.483871 0.916667
17 3GP 0.478261 0.92
18 1OR 0.474747 0.741176
19 G 0.468085 0.933333
20 5GP 0.468085 0.933333
21 7CH 0.467391 0.888889
22 6SX 0.462366 0.861111
23 6JR 0.457944 0.944444
24 G2R 0.457143 0.886076
25 GPX 0.451923 0.894737
26 GP3 0.44898 0.947368
27 2GP 0.446809 0.907895
28 GP2 0.444444 0.886076
29 GDP 0.444444 0.921053
30 GNH 0.44 0.909091
31 P2G 0.4375 0.881579
32 G2P 0.436893 0.886076
33 GMV 0.431373 0.897436
34 GTP 0.431373 0.921053
35 ALF 5GP 0.431373 0.841463
36 G1R 0.427184 0.909091
37 GCP 0.427184 0.897436
38 G3D 0.423077 0.933333
39 9GM 0.423077 0.897436
40 GSP 0.423077 0.875
41 GNP 0.423077 0.897436
42 GDP AF3 0.420561 0.841463
43 G4P 0.415094 0.933333
44 GAV 0.415094 0.886076
45 P1G 0.414141 0.87013
46 Y9Z 0.410714 0.833333
47 GCP G 0.409091 0.894737
48 GDP ALF 0.407407 0.841463
49 ALF GDP 0.407407 0.841463
50 N6R 0.40708 0.831169
51 N6S 0.40708 0.831169
52 G G 0.40708 0.947368
53 G3A 0.403509 0.947368
54 YGP 0.401786 0.876543
55 GPG 0.4 0.935065
56 G5P 0.4 0.947368
57 0O2 0.4 0.933333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2RDE; Ligand: C2E; Similar sites found with APoc: 385
This union binding pocket(no: 1) in the query (biounit: 2rde.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3IWD M2T None
2 1DR1 HBI 1.0582
3 1DR1 NAP 1.0582
4 4WUP 3UF 1.19522
5 4TWP AXI 1.19522
6 5LI9 ACP 1.19522
7 5LI1 ANP 1.19522
8 3NZ1 3NY 1.19522
9 4C5N ACP 1.19522
10 5DQ8 FLF 1.25
11 2BL9 CP6 1.2605
12 2BL9 NDP 1.2605
13 3G5D 1N1 1.59363
14 5ETJ IM5 1.59363
15 1LDM NAD 1.59363
16 2X34 UQ8 1.65746
17 4IEN GDP 1.84049
18 4L3L 5FI 1.99203
19 2QIA U20 1.99203
20 5Y72 DST 1.99203
21 5NKB 8ZT 1.99203
22 3QPB URA 1.99203
23 5FA6 NAP 1.99203
24 5FA6 FMN 1.99203
25 5FA6 FAD 1.99203
26 4ITH RCM 1.99203
27 1I7M CG 1.99203
28 2NVA PL2 1.99203
29 2WOX NDP 1.99203
30 2C49 ADN 1.99203
31 2OO0 PLP 1.99203
32 5WBF LAC 1.99203
33 5C8W PCG 2.0979
34 3EM0 CHD 2.17391
35 4YBN FAD 2.23214
36 4O9S 2RY 2.32558
37 4L9Z OXL 2.35988
38 1OUK 084 2.39044
39 4GID 0GH 2.39044
40 4LOO SB4 2.39044
41 2YAK OSV 2.39044
42 1RYD GLC 2.39044
43 2IVD ACJ 2.39044
44 4AG8 AXI 2.39044
45 3VHE 42Q 2.39044
46 5HCY 60D 2.39044
47 3KVY URA 2.39044
48 1PHK ATP 2.39044
49 3DJF BC3 2.39044
50 1T90 NAD 2.39044
51 5H2U 1N1 2.39044
52 1W8S FBP 2.39044
53 5N5U 7N8 2.39044
54 4Q4K FMN 2.39044
55 3TW1 AHN 2.53165
56 2DXU BT5 2.55319
57 1WPY BTN 2.55319
58 3UW5 MAA CHG PRO 0DQ 2.58621
59 5FPE 3TR 2.78884
60 3NKS ACJ 2.78884
61 5UIU 8CG 2.78884
62 6GWR FEW 2.78884
63 3ORK AGS 2.78884
64 6E1Q CFA 2.78884
65 5N87 N66 2.78884
66 5VC5 96M 2.78884
67 4G31 0WH 2.78884
68 5MZI FYK 2.78884
69 5MZI FAD 2.78884
70 3HAZ NAD 2.78884
71 2WME NAP 2.78884
72 4EIL NDP 2.78884
73 3I3X U22 2.78884
74 4O8A FAD 2.78884
75 4HWS 1B3 2.78884
76 1TOI HCI 2.78884
77 4D4U FUC GAL NAG 2.78884
78 4M3P HCS 2.78884
79 2X32 OTP 2.7933
80 1QKQ MAN 2.8169
81 2FZH DH1 2.91262
82 1VJY 460 3.18725
83 6B5G NAD 3.18725
84 1G51 AMP 3.18725
85 1O9J NAD 3.18725
86 4DP3 MMV 3.18725
87 4DP3 NDP 3.18725
88 4DQ2 BTX 3.18725
89 3RWP ABQ 3.18725
90 4ZUL UN1 3.18725
91 6B5G CQY 3.18725
92 2HK5 1BM 3.18725
93 3E9I XAH 3.18725
94 3LXN MI1 3.18725
95 4I3V NAD 3.18725
96 5TA6 79D 3.18725
97 4E1Z 0MX 3.18725
98 3B6R ADP 3.18725
99 5JZJ AN2 3.18725
100 5LVP ATP 3.18725
101 5JKG 6LF 3.18725
102 1K27 MTM 3.18725
103 4NZN 2OU 3.18725
104 4NZN ANP 3.18725
105 2ART LPA AMP 3.18725
106 3LGS ADE 3.18725
107 3LGS SAH 3.18725
108 4GJ3 0XP 3.18725
109 3UW4 MAA CHG PRO 0DQ 3.26087
110 5ML3 DL3 3.3557
111 3VBK COA 3.41463
112 1KRR ACO 3.44828
113 4D52 GXL 3.49206
114 4D52 GIV 3.49206
115 3PE2 E1B 3.58566
116 5W4W 9WG 3.58566
117 5DEY 59T 3.58566
118 3JU6 ANP 3.58566
119 5F3I 5UJ 3.58566
120 4KBA 1QM 3.58566
121 5WO4 B7V 3.58566
122 3PP0 03Q 3.58566
123 3EEL 53T 3.58566
124 5A3T MMK 3.58566
125 2H7C SIA 3.58566
126 4WB6 ATP 3.58566
127 1NJJ ORX 3.58566
128 2XGT NSS 3.58566
129 5LY1 PPI 3.58566
130 3HAV ATP 3.58566
131 2CSN CKI 3.58566
132 1U1F 183 3.58566
133 6EK3 OUL 3.61991
134 5TKJ ALA VAL GLY ILE GLY ALA VAL PHE 3.61991
135 4OR7 NAP 3.63636
136 1TT8 PHB 3.65854
137 2AGC DAO 3.7037
138 5TZO 7V7 3.7234
139 3RG9 NDP 3.75
140 3RG9 WRA 3.75
141 3CM2 X23 3.84615
142 3VZ3 NAP 3.98406
143 3VZ3 SSN 3.98406
144 5G48 1FL 3.98406
145 2XVD AS6 3.98406
146 1VRP ADP 3.98406
147 5L13 6ZE 3.98406
148 2R4J FAD 3.98406
149 2R4J 13P 3.98406
150 3JQ3 ADP 3.98406
151 3VRY B43 3.98406
152 5BVA FAD 3.98406
153 1U6R ADP 3.98406
154 2BJK NAD 3.98406
155 3IWJ NAD 3.98406
156 5X8G S0N 3.98406
157 2E5A LAQ 3.98406
158 6GAS FAD 3.98406
159 5VCV 1N1 3.98406
160 3G08 FEE 4.0404
161 2I8T GDD 4.19162
162 2GQS C2R 4.21941
163 5KJW 53C 4.38247
164 1OFL NGK GCD 4.38247
165 5EW9 5VC 4.38247
166 4MOB ADP 4.38247
167 4WNK 453 4.38247
168 4B0T ADP 4.38247
169 4UXL 5P8 4.38247
170 5DMZ ADP 4.38247
171 3A1I UNU 4.38247
172 2XZ9 PYR 4.38247
173 2H8H H8H 4.38247
174 5DRB 5FJ 4.38247
175 5W19 9TD 4.38247
176 5GVH FMN 4.38247
177 1GT4 UNA 4.40252
178 6GNO XDI 4.44444
179 5LJB RTL 4.44444
180 4XV1 904 4.45205
181 5YRV 5AD 4.5
182 5C83 4YN 4.54545
183 4CQE CQE 4.67626
184 1ODJ GMP 4.68085
185 4TW7 37K 4.6875
186 6BYF CIT 4.70588
187 5XVG 8FX 4.78088
188 6C0T EE4 4.78088
189 2Z3U CRR 4.78088
190 1HXD BTN 4.78088
191 5N5S NAP 4.78088
192 1M15 ADP 4.78088
193 1M15 ARG 4.78088
194 4J7H TRH 4.78088
195 6A1G 9OL 4.78088
196 4J7H TLO 4.78088
197 2QE0 NAP 4.78088
198 5FP4 YC8 4.78088
199 5UKL SIX 4.83871
200 6BE3 NAG 4.84582
201 5TVA COA 5
202 2GU8 796 5.17928
203 5BVE 4VG 5.17928
204 5HV7 RBL 5.17928
205 1RE8 BD2 5.17928
206 5U3F 7TS 5.17928
207 4BG4 ADP 5.17928
208 6FK3 PPI 5.17928
209 5WZN A2G 5.17928
210 1LDN NAD 5.17928
211 2D3M COA 5.17928
212 2XIQ MLC 5.17928
213 3A5Z KAA 5.2356
214 5XLY C2E 5.26316
215 4LRJ ANP 5.32544
216 1JE1 GMP 5.50847
217 2YKL NLD 5.55556
218 3MVH WFE 5.57769
219 4YJK URA 5.57769
220 5M90 JIF 5.57769
221 2A8Y MTA 5.57769
222 3H0L ADP 5.57769
223 3DZ6 M8E 5.57769
224 2OFV 242 5.57769
225 2BLE 5GP 5.57769
226 5VCM UDP 5.57769
227 4WOE ADP 5.57769
228 1XL8 OCB 5.57769
229 5OCG 9R5 5.82011
230 4A2A ATP 5.96659
231 4YWV SSN 5.9761
232 5IFK HPA 5.9761
233 3LVW GSH 5.9761
234 3KLJ FAD 5.9761
235 6ALW BNV 5.9761
236 6ALW BMJ 5.9761
237 1SOW NAD 5.9761
238 4PLG NAI 5.9761
239 4PLG OXM 5.9761
240 1UYY BGC BGC 6.10687
241 2GJ5 VD3 6.17284
242 4NG2 OHN 6.19469
243 4XTX 590 6.2963
244 3TCT 3MI 6.29921
245 1KGI T4A 6.29921
246 6CC0 EWM 6.32911
247 6FA4 D1W 6.35838
248 1VA6 ADP 6.3745
249 1VA6 P2S 6.3745
250 2OJW ADP 6.3745
251 3KJS NAP 6.3745
252 4FFG 0U8 6.3745
253 2IDO TMP 6.45161
254 4QAC KK3 6.45161
255 2W5P CL8 6.71141
256 1F5F DHT 6.77291
257 5AOG IAC 6.77291
258 2XMY CDK 6.77291
259 3E8N ATP 6.77291
260 3E8N VRA 6.77291
261 4I8P NAD 6.77291
262 2YAB AMP 6.77291
263 5X7Q GLC GLC 6.77291
264 1KDK DHT 6.77291
265 5HWV MBN 6.92308
266 2WLG SOP 6.97674
267 4RF7 ARG 7.17131
268 3LXK MI1 7.17131
269 1KC7 PPR 7.17131
270 3SAO DBH 7.5
271 6B3V ANP 7.56972
272 6B3V 7DQ 7.56972
273 5CPR 539 7.56972
274 5IVE 6E8 7.56972
275 4FG8 ATP 7.56972
276 2I7N ACO 7.56972
277 6EWZ APC 7.59494
278 2QHV OC9 7.61905
279 2AG4 LP3 7.92683
280 2AG4 OLA 7.92683
281 6DZN AE3 7.9646
282 1VMK GUN 7.96813
283 4ONA UW1 7.96813
284 4P8K FAD 7.96813
285 4P8K 38C 7.96813
286 3UDZ ADP 7.96813
287 5MW8 ATP 7.96813
288 1KY8 NAP 7.96813
289 4P5Z Q7M 8.36653
290 5F7J ADE 8.36653
291 5IUW IAC 8.36653
292 5IUW NAD 8.36653
293 2JLD AG1 8.36653
294 3QSB 743 8.36653
295 4Z87 GDP 8.36653
296 4QIJ 1HA 8.36653
297 1LO8 4CA 8.51064
298 1U72 NDP 8.60215
299 1U72 MTX 8.60215
300 5Y4R C2E 8.76494
301 5TUF TDC 8.76494
302 5TUF FAD 8.76494
303 3U6W KIV 8.76494
304 5L2R MLA 8.76494
305 6BQC LOP 8.76494
306 3A06 FOM 8.7766
307 1OSS BEN 8.96861
308 3CBC DBS 9.09091
309 3ESS 18N 9.13043
310 2RCU BUJ 9.16335
311 3BJE URA 9.16335
312 5XDT ZI7 9.16335
313 4OTH DRN 9.16335
314 4N70 2HX 9.16335
315 2HIM ASN 9.16335
316 1NHX FTB 9.16335
317 1NHX PEP 9.16335
318 4JGT PYR 9.16335
319 3E7O 35F 9.16335
320 5TVF CGQ 9.41177
321 2CIG 1DG 9.43396
322 1V3S ATP 9.48276
323 2IU8 PLM 9.56175
324 4KS7 X4Z 9.56175
325 4WHZ 3NL 9.56175
326 2PVN P63 9.56175
327 5A89 FMN 9.61539
328 5A89 ADP 9.61539
329 1ZB6 GST 9.96016
330 1ZB6 DIN 9.96016
331 3GC8 B45 9.96016
332 12AS AMP 10
333 2ZMF CMP 10.0529
334 1FHX 4IP 10.0775
335 3FW4 CAQ 10.1124
336 4F7E 0SH 10.2041
337 3KIH GDL 10.3093
338 2VL1 GLY GLY 10.3586
339 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 10.5263
340 5W10 CMP 10.7692
341 1LSH PLD 11.5538
342 4F4P 0SB 11.5538
343 5U19 827 11.5538
344 5U19 SAH 11.5538
345 3E2M E2M 11.8919
346 1F9V ADP 11.9522
347 1SDW IYT 11.9522
348 3EFS BTN 12.0172
349 2RHQ GAX 12.3506
350 4YRI 4JH 12.3506
351 3RUG DB6 12.4481
352 1AOE NDP 12.5
353 1AOE GW3 12.5
354 5H9P TD2 12.6582
355 4R3U 3KK 12.6582
356 4R3U 3HC 12.6582
357 4FE2 AIR 12.749
358 5H9Y BGC BGC BGC BGC 13.1474
359 4LAE NAP 13.1737
360 4LAE 1VM 13.1737
361 4Y24 TD2 13.6364
362 5D48 L96 13.8158
363 3OV6 MK0 13.9442
364 1Q8Y ADP 14.741
365 2QHS OCA 15.6118
366 2CJU PHX 15.7025
367 5FUI APY 16.6667
368 5T7I LAT NAG GAL 16.7742
369 5M6N 7H9 17.7966
370 2REG CHT 17.9283
371 1REQ DCA 17.9283
372 5LRT ADP 18.3267
373 3PVW QRX 18.9189
374 1SBR VIB 20
375 5CIC 51R 22.2222
376 2JDR L20 22.3108
377 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 22.3108
378 4MTI 2DX 22.6087
379 1HFE CYS 23.5772
380 4L9I 8PR 25.498
381 4X6F 3XU 25.7143
382 4WO4 JLS 27
383 5WL1 D3D 27.2727
384 5WL1 CUY 27.2727
385 5U98 1KX 27.2727
Pocket No.: 2; Query (leader) PDB : 2RDE; Ligand: C2E; Similar sites found with APoc: 65
This union binding pocket(no: 2) in the query (biounit: 2rde.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4NAE 1GP 0.888889
2 4OYA 1VE 1.99203
3 5AE2 FYC 1.99203
4 5AE2 FAD 1.99203
5 5EYK 5U5 1.99203
6 5H4S RAM 1.99203
7 4MIB 28M 2.39044
8 6GAR FAD 2.39044
9 5MW4 5JU 2.39044
10 4WZ8 3W7 2.39044
11 1VKF CIT 2.39044
12 2Y6O 1N1 2.78884
13 4HWT 1B2 2.78884
14 3FC2 IBI 2.78884
15 6D6L FY4 2.94118
16 5TWB FAD 3.18725
17 1OX5 1PR 3.18725
18 1G51 AMO 3.18725
19 3HCH RSM 3.42466
20 3A7R LAQ 3.58566
21 1VPV PLM 3.58566
22 5ODY 9SK 3.62319
23 1X54 4AD 3.98406
24 1IIM TTP 3.98406
25 5LYH 7B8 4.14508
26 2Z9I GLY ALA THR VAL 4.32099
27 3IA4 NDP 4.32099
28 3TKI S25 4.33437
29 6CEP NAD 4.38247
30 6CEP OXM 4.38247
31 5NDF UDP 4.38247
32 3LZW FAD 4.38247
33 4QYN RTL 4.51128
34 1E1O LYS 4.78088
35 3I9U DTU 5.17928
36 6GH9 MIX 5.17928
37 6MVU K4V 5.57769
38 1B7Y FYA 5.57769
39 4PLT NAI 5.57769
40 4PLT OXM 5.57769
41 3ICR FAD 5.57769
42 3K0T BGC 6.29371
43 4U0I 0LI 6.3745
44 1TIQ COA 6.66667
45 3HKW IX6 6.77291
46 1JG3 ADN 6.80851
47 3UYK 0CX 7.23514
48 2EB5 OXL 7.96813
49 5GP0 GPP 8.05369
50 1ZNY GDP 8.69565
51 1GPM AMP 9.16335
52 4NV7 COA 9.16335
53 3QFS FAD 9.16335
54 3QFS NAP 9.16335
55 2W9S NDP 9.93789
56 4YVN EBS 9.96016
57 1J3I NDP 9.96016
58 1J3I WRA 9.96016
59 4CS4 AXZ 11.5538
60 1S3G AP5 11.9816
61 3WG3 A2G GAL NAG FUC 12.3596
62 5KD6 6C7 13.1474
63 5HES 032 13.1474
64 1WZ1 DNS 17.6991
65 5OQW A4E 19.685
APoc FAQ
Feedback