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Receptor
PDB id Resolution Class Description Source Keywords
5EJL 2.3 Å NON-ENZYME: OTHER MRKH, A NOVEL C-DI-GMP DEPENDENCE TRANSCRIPTION REGULATORY F KLEBSIELLA PNEUMONIAE COMPLEX C-DI-GMP PILZ DOMAIN DNA BINDING PROTEIN
Ref.: THE PILZ DOMAIN OF MRKH REPRESENTS A NOVEL DNA BIND PROTEIN CELL V. 7 766 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:303;
A:305;
A:304;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
C2E A:301;
A:302;
Valid;
Valid;
none;
none;
Kd = 0.24 uM
690.411 C20 H24 N10 O14 P2 c1nc2...
EDO A:308;
A:307;
A:306;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EJL 2.3 Å NON-ENZYME: OTHER MRKH, A NOVEL C-DI-GMP DEPENDENCE TRANSCRIPTION REGULATORY F KLEBSIELLA PNEUMONIAE COMPLEX C-DI-GMP PILZ DOMAIN DNA BINDING PROTEIN
Ref.: THE PILZ DOMAIN OF MRKH REPRESENTS A NOVEL DNA BIND PROTEIN CELL V. 7 766 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5EJL Kd = 0.24 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 5EJL Kd = 0.24 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 5EJL Kd = 0.24 uM 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 : 5EJL; Ligand: C2E; Similar sites found with APoc: 369
This union binding pocket(no: 1) in the query (biounit: 5ejl.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3TCT 3MI None
2 2GJ5 VD3 None
3 3EFS BTN None
4 6D6L FY4 None
5 1TT8 PHB 0.806452
6 4BFM ANP 0.806452
7 4IEN GDP 1.22699
8 1WPY BTN 1.2766
9 4MIB 28M 1.6129
10 1RYD GLC 1.6129
11 2F6U CIT 1.7094
12 3PE2 E1B 1.78042
13 5BVE 4VG 2.01613
14 5N87 N66 2.01613
15 3K56 IS3 2.01613
16 1V97 FAD 2.01613
17 3JU6 ANP 2.01613
18 1YFS ALA 2.01613
19 2IVD ACJ 2.01613
20 1KDK DHT 2.01613
21 1PHK ATP 2.01613
22 2VL1 GLY GLY 2.01613
23 6MPT C30 2.01613
24 2QX0 PH2 2.01613
25 2OO0 PLP 2.01613
26 1KGI T4A 2.3622
27 6C0T EE4 2.41935
28 3ZXR P3S 2.41935
29 3ZXR IQ1 2.41935
30 5AE2 FYC 2.41935
31 5HCY 60D 2.41935
32 5AE2 FAD 2.41935
33 5LRT ADP 2.41935
34 3PP0 03Q 2.41935
35 3AI7 TPP 2.41935
36 3GD9 GLC BGC BGC BGC 2.41935
37 5CPR 539 2.41935
38 3GNI ATP 2.41935
39 5ABH YWN 2.41935
40 3BJE URA 2.41935
41 2R5V HHH 2.41935
42 2RAB FAD 2.41935
43 1O9J NAD 2.41935
44 1C1X HFA 2.41935
45 2GQS C2R 2.53165
46 2DXU BT5 2.55319
47 4ZCC FAD 2.67857
48 4DQ2 BTX 2.7439
49 5TA6 79D 2.7933
50 5KJW 53C 2.82258
51 4XTX 590 2.82258
52 1VA6 P2S 2.82258
53 1VA6 ADP 2.82258
54 1F9V ADP 2.82258
55 4B0T ADP 2.82258
56 4CJN QNZ 2.82258
57 2OJW ADP 2.82258
58 3ZJX BOG 2.82258
59 3NEM AMO 2.82258
60 4Z87 GDP 2.82258
61 1XL8 OCB 2.82258
62 4EWH T77 2.82258
63 1Q8Y ADP 2.82258
64 5JIC ADP 2.82258
65 5JIC N7E 2.82258
66 1C3X 8IG 2.82258
67 3RG9 NDP 2.91667
68 5DQ8 FLF 2.91667
69 2I8T GDD 2.99401
70 3DGY 2GP 3.09278
71 3LVW GSH 3.22581
72 3B6R ADP 3.22581
73 6E1Q CFA 3.22581
74 5U3F 7TS 3.22581
75 4HWS 1B3 3.22581
76 1U6R ADP 3.22581
77 4LOO SB4 3.22581
78 1A5Z FBP 3.22581
79 5EOB 5QQ 3.22581
80 1OX5 1PR 3.22581
81 1M5B BN1 3.22581
82 4E1Z 0MX 3.22581
83 1GPM AMP 3.22581
84 2C5A NAD 3.22581
85 2C5A GDC 3.22581
86 3I3X U22 3.22581
87 3NKS ACJ 3.22581
88 4OTH DRN 3.22581
89 5DMZ ADP 3.22581
90 3OZ2 FAD 3.22581
91 5KD6 LBU 3.22581
92 6CC0 EWM 3.37553
93 1ZOS MTM 3.47826
94 4MOB ADP 3.62903
95 5HV7 RBL 3.62903
96 4CS4 ANP 3.62903
97 5Y72 DST 3.62903
98 3LXN MI1 3.62903
99 3JQ3 ADP 3.62903
100 3RWP ABQ 3.62903
101 1M15 ADP 3.62903
102 1M15 ARG 3.62903
103 4BG4 ADP 3.62903
104 5W4W 9WG 3.62903
105 6BE3 NAG 3.62903
106 1J3I WRA 3.62903
107 5LVP ATP 3.62903
108 5XDT MB3 3.62903
109 4KBA 1QM 3.62903
110 4CQE CQE 3.62903
111 6ALW BMJ 3.62903
112 1X54 4AD 3.62903
113 1I7M CG 3.62903
114 4CS4 AXZ 3.62903
115 3DZ6 M8E 3.62903
116 4GJ3 0XP 3.62903
117 2C49 ADN 3.62903
118 5XDT ZI7 3.62903
119 2RKV ZBA 3.62903
120 3LGS ADE 3.62903
121 1JGT CMA 3.62903
122 2AG4 OLA 3.65854
123 2AG4 LP3 3.65854
124 5X8G S0N 3.71134
125 1UYY BGC BGC 3.81679
126 1MAI I3P 3.81679
127 3CM2 X23 3.84615
128 4GID 0GH 3.86598
129 4RF7 ARG 4.03226
130 1YXM ADE 4.03226
131 2YAK OSV 4.03226
132 3LXK MI1 4.03226
133 6EWZ APC 4.03226
134 2QIA U20 4.03226
135 2YNE YNE 4.03226
136 2YNE NHW 4.03226
137 2JLD AG1 4.03226
138 4WOE ADP 4.03226
139 12AS AMP 4.03226
140 4PAB THG 4.03226
141 2J3M ATP 4.03226
142 3MVH WFE 4.09357
143 5TZO 7V7 4.25532
144 5G48 1FL 4.43548
145 5EW9 5VC 4.43548
146 1OFL NGK GCD 4.43548
147 1REQ DCA 4.43548
148 3B2Q ATP 4.43548
149 2CSN CKI 4.43548
150 5VC5 96M 4.43548
151 2GMH UQ5 4.43548
152 4WZ8 3W7 4.43548
153 5MW4 5JU 4.43548
154 3VZ3 SSN 4.43548
155 5ZYN FAD 4.4586
156 3OYW TDG 4.47761
157 1SBR VIB 4.5
158 5C83 4YN 4.54545
159 6FA4 D1W 4.62428
160 5CIC 51R 4.62963
161 2E0N SAH 4.6332
162 5ML3 DL3 4.69799
163 2Z3U CRR 4.70588
164 1VKF CIT 4.78723
165 3HCH RSM 4.79452
166 4L3L 5FI 4.83871
167 4OYA 1VE 4.83871
168 4WNK 453 4.83871
169 4B2Z P5S 4.83871
170 1VJY 460 4.83871
171 6CGD GNP 4.83871
172 1D4D FAD 4.83871
173 4X3R 686 4.83871
174 5FPE 3TR 4.83871
175 3IES M24 4.83871
176 4RD0 GDP 4.83871
177 3PGU OLA 4.83871
178 2YYE APC 4.83871
179 4WHZ 3NL 4.83871
180 4I9B NAD 4.83871
181 4UX9 ANP 4.83871
182 5IUW NAD 4.83871
183 2GJN FMN 4.83871
184 1ZB6 GST 4.88599
185 1ZB6 DIN 4.88599
186 4NAE 1GP 4.88889
187 1C3V PDC 4.89796
188 4L9I 8PR 4.96032
189 2WLG SOP 5.11628
190 2VSL MAA LYS PRO PHE 5.20833
191 1W6P NDG GAL 5.22388
192 2QHV OC9 5.24194
193 5DEY 59T 5.24194
194 1T36 ORN 5.24194
195 2YC5 6BC 5.24194
196 5TVF CGQ 5.24194
197 1WPQ 13P 5.24194
198 5H2U 1N1 5.24345
199 1VRP ADP 5.51181
200 5Y4R C2E 5.51724
201 3SAO DBH 5.625
202 3SAO NKN 5.625
203 3QSB 743 5.64516
204 3GC8 B45 5.64516
205 4N70 2HX 5.64516
206 1PN4 HDC 5.64516
207 2NVA PL2 5.64516
208 4DXD 9PC 5.64516
209 1C5C TK4 5.64516
210 1IA9 ANP 5.71429
211 3KV8 FAH 5.7554
212 4KS7 X4Z 5.82192
213 5XLY C2E 6.01504
214 1V3S ATP 6.03448
215 5WO4 B7V 6.04839
216 3V8S 0HD 6.04839
217 2XIQ MLC 6.04839
218 5JBX MLI 6.04839
219 5F3I 5UJ 6.04839
220 5FA6 FAD 6.04839
221 5FA6 FMN 6.04839
222 5FA6 NAP 6.04839
223 5UR1 YY9 6.04839
224 5HW4 SAM 6.04839
225 4FG8 ATP 6.04839
226 3TWD GOB 6.04839
227 2GVJ DGB 6.04839
228 3NZ1 3NY 6.04839
229 4ITH RCM 6.04839
230 3RUG DB6 6.06061
231 4NG2 OHN 6.19469
232 5M90 JIF 6.45161
233 1OUK 084 6.45161
234 1SDW IYT 6.45161
235 4YSW NAI 6.45161
236 4YSW FAD 6.45161
237 1Q9I FAD 6.45161
238 1Q9I TEO 6.45161
239 4YRI 4JH 6.45161
240 5J5R IMP 6.45161
241 5J5R 6G1 6.45161
242 3K8D KDO 6.45161
243 1Q19 APC 6.45161
244 3DLG GWE 6.45161
245 1VPV PLM 6.45161
246 1HFE CYS 6.50407
247 6DZN AE3 6.63717
248 4X6F 3XU 6.66667
249 1G51 AMO 6.85484
250 1G51 AMP 6.85484
251 2YAB AMP 6.85484
252 3DUV KDO 6.85484
253 5OCG 9R5 6.87831
254 2TPI ILE VAL 6.89655
255 5N0L ILE 6.91824
256 5HWV MBN 6.92308
257 1QKQ MAN 7.04225
258 5WL1 CUY 7.07071
259 5WL1 D3D 7.07071
260 5U98 1KX 7.07071
261 1LSH PLD 7.25806
262 3E9I XAH 7.25806
263 2ZMF CMP 7.25806
264 2HK5 1BM 7.25806
265 3VRY B43 7.25806
266 5C5H 4YB 7.25806
267 4QAC KK3 7.25806
268 6A1G 9OL 7.25806
269 5YZ2 AMP 7.63889
270 3E8N ATP 7.66129
271 3E8N VRA 7.66129
272 5LI1 ANP 7.66129
273 2QBU SAH 7.75862
274 2XG5 EC2 7.79817
275 2XG5 EC5 7.79817
276 3EM0 CHD 7.97101
277 4WO4 JLS 8.06452
278 6GWR FEW 8.06452
279 4P5Z Q7M 8.06452
280 4ONA UW1 8.06452
281 2E5A LAQ 8.06452
282 2XMY CDK 8.06452
283 6C8X BVR 8.08081
284 3OV6 MK0 8.46774
285 2RCU BUJ 8.46774
286 2ART LPA AMP 8.46774
287 2RHQ GAX 8.46774
288 3A16 PXO 8.46774
289 4QIJ 1HA 8.46774
290 2PLK P3D 8.46774
291 4DQL NAP 8.46774
292 2AJH MET 8.67347
293 5TVA COA 8.75
294 3IWD M2T 8.82353
295 2BOS GLA GAL GLC 8.82353
296 2QHS OCA 8.86076
297 5XVG 8FX 8.87097
298 5UIU 8CG 8.87097
299 4NV7 COA 8.87097
300 3TTC ADP 8.87097
301 5L2R MLA 8.87097
302 3QFS FAD 8.87097
303 3QFS NAP 8.87097
304 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 9.06433
305 2JDR L20 9.06433
306 5A5W GUO 9.09091
307 5TUF TDC 9.27419
308 3A5Z KAA 9.45122
309 3UW5 MAA CHG PRO 0DQ 9.48276
310 5TKJ ALA VAL GLY ILE GLY ALA VAL PHE 9.50226
311 2PVN P63 9.67742
312 2HIM ASN 9.67742
313 2YKL NLD 9.90566
314 4R3U 3KK 10.0806
315 4R3U 3HC 10.0806
316 3O9L LPN 10.0806
317 3G5D 1N1 10.4839
318 3C3N FMN 10.4839
319 2W5P CL8 10.7383
320 2CJU PHX 10.7438
321 3A7R LAQ 10.8871
322 1B7Y FYA 10.8871
323 6B3V ANP 11.2903
324 6B3V 7DQ 11.2903
325 3G1Z AMP 11.2903
326 5LYH 7B8 11.399
327 5JZJ AN2 11.6935
328 4FE2 AIR 11.7647
329 6GNO XDI 11.8519
330 4DDY DN6 12.0968
331 5F7J ADE 12.0968
332 4BMX ADE 12.5
333 5LJB RTL 12.5926
334 1XXA ARG 12.8205
335 4O9S 2RY 13.0233
336 3ESS 18N 13.0435
337 3CBC DBS 13.1313
338 2AGC DAO 13.5802
339 4Y24 TD2 13.6364
340 1HXD BTN 13.7097
341 3PVW QRX 14.1129
342 5UKL SIX 14.1129
343 4FL3 ANP 14.1129
344 4TWP AXI 14.5161
345 1ZNY GDP 14.5161
346 3FW4 CAQ 14.6067
347 3GQI ACP 14.9194
348 5YRV 5AD 14.9194
349 2GU8 796 16.129
350 1RE8 BD2 16.129
351 4WB6 ATP 16.129
352 2QCS ANP 16.129
353 3FHI ANP 16.129
354 5H9Y BGC BGC BGC BGC 16.129
355 4WB7 ATP 16.129
356 4F7E 0SH 16.3265
357 5OQW A4E 16.5354
358 2X34 UQ8 16.5746
359 2XGT NSS 16.7816
360 2IU8 PLM 16.9355
361 5M6N 7H9 17.7966
362 2X32 OTP 17.8771
363 3H0L ADP 19.1489
364 3A5Y KAA 19.3548
365 4EWN 0VR 19.3548
366 5FUI APY 22.7273
367 2I4O ATP 26.2097
368 5FKP 6UL 27.2727
369 5ODY 9SK 28.9855
Pocket No.: 2; Query (leader) PDB : 5EJL; Ligand: C2E; Similar sites found with APoc: 15
This union binding pocket(no: 2) in the query (biounit: 5ejl.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 1M7G AV2 1.4218
2 4FK7 P34 2.18341
3 1RJW ETF 2.82258
4 6F97 FAD 2.82258
5 3HQ9 OXL 2.82258
6 2WSA 646 2.96804
7 2WSA MYA 2.96804
8 4URF 1PS 4.03226
9 5LNW RP5 4.03226
10 6FTB M0E 5.71429
11 5F1V 3VN 6.39731
12 2BHZ MAL 8.06452
13 3BP1 GUN 8.06452
14 4NPT 017 8.08081
15 2BOS GLA GAL GLC NBU 8.82353
Pocket No.: 3; Query (leader) PDB : 5EJL; Ligand: C2E; Similar sites found with APoc: 9
This union binding pocket(no: 3) in the query (biounit: 5ejl.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2QTZ NAP 2.82258
2 1MFI FHC 4.38596
3 1GTE IUR 4.83871
4 1GTE FMN 4.83871
5 3F6R FMN 6.08108
6 4BTV RB3 7.66129
7 4P8K FAD 8.06452
8 4P8K 38C 8.06452
9 2Y6Q I7T 8.46774
Pocket No.: 4; Query (leader) PDB : 5EJL; Ligand: C2E; 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: 5ejl.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5EJL; Ligand: C2E; Similar sites found with APoc: 1
This union binding pocket(no: 5) in the query (biounit: 5ejl.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 1ESM COA 3.79747
Pocket No.: 6; Query (leader) PDB : 5EJL; Ligand: C2E; 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: 5ejl.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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