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Receptor
PDB id Resolution Class Description Source Keywords
6GMN 1.94 Å NON-ENZYME: OTHER PVHL:ELOB:ELOC IN COMPLEX WITH METHYL 4H-FURO[3,2-B]PYRROLE- CARBOXYLATE HOMO SAPIENS E3 UBIQUITIN LIGASE TUMOR SUPRESSOR PROTAC FRAGMENT-BASEDDISCOVERY ONCOPROTEIN
Ref.: SURFACE PROBING BY FRAGMENT-BASED SCREENING AND COMPUTATIONAL METHODS IDENTIFIES LIGANDABLE POCKETS VON HIPPEL-LINDAU (VHL) E3 UBIQUITIN LIGASE. J. MED. CHEM. V. 61 7387 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT F:301;
C:301;
A:201;
I:301;
L:301;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
F4E B:201;
K:201;
Valid;
Valid;
none;
none;
submit data
165.146 C8 H7 N O3 COC(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6GMN 1.94 Å NON-ENZYME: OTHER PVHL:ELOB:ELOC IN COMPLEX WITH METHYL 4H-FURO[3,2-B]PYRROLE- CARBOXYLATE HOMO SAPIENS E3 UBIQUITIN LIGASE TUMOR SUPRESSOR PROTAC FRAGMENT-BASEDDISCOVERY ONCOPROTEIN
Ref.: SURFACE PROBING BY FRAGMENT-BASED SCREENING AND COMPUTATIONAL METHODS IDENTIFIES LIGANDABLE POCKETS VON HIPPEL-LINDAU (VHL) E3 UBIQUITIN LIGASE. J. MED. CHEM. V. 61 7387 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 6GMN - F4E C8 H7 N O3 COC(=O)c1c....
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 6GMN - F4E C8 H7 N O3 COC(=O)c1c....
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 6GMN - F4E C8 H7 N O3 COC(=O)c1c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: F4E; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 F4E 1 1
2 4P5 0.568182 0.8125
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6GMN; Ligand: F4E; Similar sites found with APoc: 389
This union binding pocket(no: 1) in the query (biounit: 6gmn.bio4) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1UVC STE None
3 2WAT COA None
4 3ND6 ATP 1.75439
5 4O4Z N2O 2.88462
6 1XZ3 ICF 3.08642
7 5V13 JH3 3.08642
8 3UCJ AZM 4.12371
9 2BHW LUX 4.32099
10 5G3N X28 4.72441
11 3N7H DE3 4.80769
12 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 4.80769
13 3OGN 3OG 4.80769
14 2O5L MNR 4.80769
15 1JQY A32 4.85437
16 4EMV 0R9 4.93827
17 4BNU 9KQ 4.93827
18 2FR3 REA 5.15464
19 5IXK 6EW 5.15464
20 4NB5 2JT 5.15464
21 3KDU NKS 5.15464
22 2NPA MMB 5.15464
23 5KO8 FMN 5.15464
24 5KO8 IYR 5.15464
25 1K7L 544 5.20833
26 4GCZ FMN 5.55556
27 5YZ2 AMP 5.55556
28 5NM7 GLY 5.55556
29 4INW 1EY 5.71429
30 3MBG FAD 5.7554
31 4TQ3 GPP 5.76923
32 3LU1 NAD 5.76923
33 4U0S ADP 5.76923
34 1GV0 NAD 5.76923
35 4XB4 45D 5.92105
36 4UNR QZE 6.17284
37 2E9L OLA 6.17284
38 2E9L BGC 6.17284
39 2E9L PLM 6.17284
40 3X01 AMP 6.17284
41 1YC4 43P 6.17284
42 1YMT DR9 6.17284
43 5B25 4QJ 6.17284
44 1YP0 PEF 6.17284
45 2IHU TP9 6.18557
46 1FM9 9CR 6.18557
47 4M8E 29V 6.18557
48 3H0A 9RA 6.18557
49 4OHU 2TK 6.18557
50 4OHU NAD 6.18557
51 4PGK Y69 6.18557
52 5K53 STE 6.18557
53 3V66 D3A 6.18557
54 1BGQ RDC 6.18557
55 6AD9 KK4 6.18557
56 3GB5 FMN 6.18557
57 4O1Z MXM 6.18557
58 5F5N 5VD 6.18557
59 3U5S FAD 6.34921
60 3H2B SAH 6.40394
61 2YLN CYS 6.73077
62 6BA2 7KM 6.73077
63 6HH6 A3R 6.73077
64 3KFC 61X 6.73077
65 3EVF GTA 6.73077
66 1KUK PCA LYS TRP 6.73077
67 3HLX PQQ 6.79012
68 1OLM VTQ 6.79012
69 4J24 EST 6.79012
70 1U3R 338 6.79012
71 1O6U PLM 6.79012
72 4E1M TQ2 6.79012
73 1GUZ NAD 6.79012
74 3LCC SAH 6.79012
75 1JR8 FAD 6.83761
76 1YYE 196 7.2165
77 4E70 N7I 7.2165
78 5UC9 MYR 7.2165
79 1XRO LEU 7.2165
80 1J54 TMP 7.2165
81 4WKI 3PW 7.2165
82 1VR0 3SL 7.2165
83 2IDO TMP 7.22892
84 4V2O CLQ 7.31707
85 5DF1 58X 7.40741
86 5DF1 NAP 7.40741
87 3FAL REA 7.40741
88 5A4W QCT 7.40741
89 3TGE TGE 7.69231
90 1G2N EPH 7.69231
91 3WCA FPS 7.69231
92 3SHZ 5CO 7.69231
93 5B4B LP5 7.69231
94 5JF2 SF7 7.69231
95 2R75 01G 7.69231
96 2RH4 EMO 8.02469
97 1HG4 LPP 8.24742
98 5J32 IPM 8.24742
99 2PX6 DH9 8.24742
100 2OCI TYC 8.24742
101 1YOK P6L 8.24742
102 5UNJ RJW 8.24742
103 2R0N FAD 8.24742
104 2GFD RDA 8.64198
105 6D28 NEC 8.64198
106 3VZ3 SSN 8.64198
107 3SFI 3SF 8.65385
108 5XDT GDP 8.65385
109 5XDT MB3 8.65385
110 1PZO CBT 8.65385
111 2Q1H AS4 8.65385
112 2P1C GG3 8.65385
113 3L1N PLM 8.65385
114 1L0I PSR 8.97436
115 4MRV HGD 9.25926
116 4MRP GSH 9.25926
117 4MRS GDS 9.25926
118 4B52 RDF 9.25926
119 1A05 IPM 9.27835
120 3D9F N6C 9.27835
121 4JD3 PLM 9.27835
122 4JD3 COA 9.27835
123 4FWE FAD 9.27835
124 2C0U FAD NBT 9.27835
125 1ZED PNP 9.27835
126 3ROE THM 9.27835
127 1H9G COA MYR 9.27835
128 3RO7 TDR 9.27835
129 5VRH OLC 9.27835
130 1DQE BOM 9.48905
131 4U0I 0LI 9.61539
132 3CR3 ADP 9.61539
133 1GZ4 ATP 9.61539
134 1N1G BCP 9.61539
135 1XM4 PIL 9.87654
136 3HY2 ATP 10
137 2ZE7 AMP 10.2767
138 3OKI OKI 10.3093
139 3U4C NDP 10.3093
140 4GFD 0YB 10.3093
141 1XAJ NAD 10.3093
142 1XAJ CRB 10.3093
143 6F8B CXH 10.3093
144 5W8Q BU4 10.3093
145 1MVN PCO 10.4938
146 6BJA COA 10.4938
147 3P7N FMN 10.4938
148 4V24 GYR 10.5121
149 4CQE CQE 10.5769
150 2R40 EPH 10.5769
151 5Y24 GLY MET PRO ARG GLY ALA 10.5769
152 5YVR NDP 10.5769
153 4LY9 S6P 10.5769
154 4LY9 1YY 10.5769
155 2R40 20E 10.5769
156 1NRL SRL 10.5769
157 3ZUY TCH 10.5769
158 3K05 SEP GLN GLU TYR NH2 10.5769
159 2P41 G1G 10.5769
160 6FX0 E9T 10.5769
161 1M13 HYF 10.5769
162 4R38 RBF 10.7143
163 3CYI ATP 10.9091
164 3D78 NBB 10.9244
165 2OHV NHL 11.1111
166 4MG7 27H 11.1111
167 3ICS COA 11.1111
168 3UUD EST 11.1111
169 2XCU C5P 11.1111
170 2QA8 GEN 11.1111
171 5AAV GW5 11.1111
172 3ICT COA 11.1111
173 5DX3 EST 11.1111
174 5WGD EST 11.1111
175 4MG9 27K 11.1111
176 2BJ4 OHT 11.1111
177 2QZO KN1 11.1111
178 5DXG EST 11.1111
179 3E3U NVC 11.1111
180 3ZVS MLI 11.3402
181 6BWL UDP 11.3402
182 3KP6 SAL 11.3402
183 4RPO T6C 11.3402
184 5FUS DAO 11.5385
185 6AYI C3G 11.5385
186 1ZDT PEF 11.5385
187 2WKQ FMN 11.5385
188 4QJR PIZ 11.5385
189 6A46 DCM 11.5385
190 1LTT GAL BGC 11.5385
191 5OLK DTP 11.5385
192 4I4B 1CV 11.7284
193 4ZVI 4S4 11.7284
194 1WY7 SAH 11.7284
195 1LEK GLU GLN TYR LYS PHE TYR SER VAL 11.7284
196 5BVE 4VG 11.7284
197 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 12
198 2GTE VA 12.0968
199 5TUX ECH 12.3457
200 1TIQ COA 12.3457
201 1LVK MNT BEF 12.3711
202 4U8P FDA 12.3711
203 4U8P UDP 12.3711
204 4DL8 UMP AF3 PO4 12.3711
205 2HJ3 FAD 12.3711
206 5FMD NYT 12.3711
207 4IBF 1D5 12.4031
208 2NU8 COA 12.5
209 4XOQ F42 12.5
210 3BJC WAN 12.5
211 5AZC PGT 12.5
212 5LX9 OLB 12.5
213 1OJ7 NZQ 12.5
214 5LWY OLB 12.5
215 4D7M TDC 12.5
216 5LWY OLA 12.5
217 1FK5 OLA 12.9032
218 4LRZ ADP 12.963
219 3PNL ADP 12.963
220 2W14 WR2 12.963
221 1RDT L79 13.0435
222 3RMK BML 13.253
223 1PFK ADP 13.4021
224 3I51 6PL 13.4021
225 4D79 ATP 13.4021
226 4KCF AKM 13.4021
227 5NWI TYR PHE SER SEP ASN 13.4021
228 4RDI ATP 13.4021
229 1NF8 BOG 13.4021
230 2NXW TPP 13.4021
231 3NT6 COA 13.4615
232 3NTD COA 13.4615
233 3NTA COA 13.4615
234 1YS4 NAP 13.4615
235 2J1P GRG 13.4615
236 4FR3 0V4 13.4615
237 3KYO LYS LEU PRO ALA GLN PHE TYR ILE LEU 13.4615
238 2WCJ M21 13.4615
239 2FV5 541 13.4615
240 3RDE OYP 13.4615
241 1TMX HGX 13.4615
242 3E70 GDP 13.4615
243 1QNF FAD 13.4615
244 1T36 U 13.4615
245 5U97 PIT 13.4615
246 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 13.4615
247 1BKC INN 13.4615
248 5J60 FAD 13.5802
249 2OO8 RAJ 13.5802
250 1JAY F42 13.5802
251 4IHL 1F5 13.8889
252 3RS8 ALA TRP LEU PHE GLU ALA 14.1975
253 2VDV SAM 14.1975
254 3EWK FAD 14.1975
255 4NAT ADP 14.375
256 4NAT 2W5 14.375
257 4EKQ NPO 14.4231
258 5TPR NAD 14.4231
259 4O6W ACE PRO LEU 2SO SER TPO NH2 14.4231
260 5TO8 7FM 14.433
261 2QJY SMA 14.433
262 5UC4 83S 14.433
263 5LPA ATP 14.433
264 5LPA 71R 14.433
265 2Z7I 742 14.433
266 5F2T PLM 14.433
267 2QQD AG2 15.0943
268 2QQC AG2 15.0943
269 1T0S BML 15.1163
270 4RW3 PLM 15.3846
271 1DMH LIO 15.3846
272 1N13 AG2 15.3846
273 1YUC EPH 15.3846
274 1HK8 DGT 15.3846
275 4RW3 TDA 15.3846
276 1MT1 AG2 15.3846
277 3DMH SAM 15.3846
278 6GBV FMN 15.3846
279 5FM0 WAQ 15.4321
280 1OPK MYR 15.4321
281 5ICK FEZ 15.4639
282 3I59 N6R 15.4639
283 6A5Y 9CR 15.4639
284 3P5P A3C 15.4639
285 5VZ0 2BA 15.4639
286 1B7A OPE 15.4639
287 3OJI PYV 15.4639
288 5HVA DUP 15.7143
289 2A06 SMA 16.0494
290 5WP5 SAH 16.0494
291 1MOQ GLP 16.0494
292 5ZM4 9FU 16.3462
293 5ZM4 AKG 16.3462
294 3HAD NAD 16.3462
295 4LSJ LSJ 16.3462
296 1NHZ 486 16.3462
297 5UC1 486 16.3462
298 4IVG ANP 16.4948
299 4IPE ANP 16.4948
300 1VLH PNS 16.6667
301 2ZKJ ADP 17.3077
302 1M7G ADP 17.5258
303 1M7G ADX 17.5258
304 2DQA NAG NAG NAG 17.5258
305 1LSH PLD 17.5258
306 3RLF MAL 17.5258
307 2DYS TGL 17.9012
308 5Z84 TGL 17.9012
309 2DYR TGL 17.9012
310 5ZCO PEK 17.9012
311 2DYR PEK 17.9012
312 2DYS PEK 17.9012
313 5ZCO TGL 17.9012
314 2YAY DUP 17.9012
315 2Y69 CHD 17.9012
316 5Z84 CHD 17.9012
317 1ATL 0QI 17.9012
318 5ZCO CHD 17.9012
319 3V78 ET 18.2692
320 3FRQ ERY 18.2692
321 2YYJ 4HP 18.5185
322 2YYJ FAD 18.5185
323 1MUU NAD 18.5567
324 1MV8 NAD 18.5567
325 6MPT C30 18.5567
326 1XX4 BAM 18.5567
327 2NXE SAM 19.1358
328 3DFR NDP 19.1358
329 1UHK CZN 19.2308
330 3WDM ADN 19.2308
331 4P8O 883 19.2308
332 5YJF 8WO 19.2308
333 5K4W THR 19.5876
334 1ZQ9 SAM 19.5876
335 4RHE FMN 20.1923
336 2CE7 ADP 20.1923
337 4K2G 1OQ 20.6186
338 1DQS CRB 20.6186
339 1DQS NAD 20.6186
340 3ZOK NAD 20.6186
341 4ASE AV9 20.6186
342 3GDH SAH 20.6186
343 3TTZ 07N 21.1538
344 2J7T 274 21.1538
345 6BMS PLM 21.6495
346 4OGQ 7PH 21.6495
347 2PEZ DAT 22.1154
348 2PEZ GGZ 22.1154
349 2OFW ADX 22.1154
350 1N9L FMN 22.1154
351 4QC6 30N 23.0769
352 5EKO N17 23.0769
353 3CX5 SMA 23.7113
354 2IBZ SMA 23.7113
355 1YBH CIE 23.7113
356 3CXH SMA 23.7113
357 5U98 1KX 24.0385
358 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 24.0385
359 1D6H COA 24.0385
360 5T70 THR SER ASN LEU GLN GLU GLN ILE GLY TRP 24.0385
361 3PT9 SAH 24.7423
362 2FP2 TSA 24.7423
363 1EZV SMA 24.7423
364 2UXI G50 25
365 3JRX S1A 25.3086
366 2I80 G1L 26.5432
367 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 26.8041
368 4R6W PC 26.8041
369 3W54 RNB 26.8041
370 2PX8 MGT 26.9231
371 5HM3 649 27.8846
372 5MWY YNU 27.8846
373 4UDB CV7 27.8846
374 2A3I C0R 27.8846
375 5HCV 60R 27.8846
376 1C1D PHE 28.3951
377 1N8V BDD 28.5714
378 3RY9 1CA 28.8462
379 4PJT 2YQ 28.8462
380 4QTB 38Z 28.866
381 4P6X HCY 29.8077
382 3GN8 DEX 29.8077
383 5JZI LYS LEU VAL ALA LEU GLY ILE ASN ALA VAL 31.9588
384 5C0C ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 31.9588
385 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 31.9588
386 2X4T ASN LEU VAL PRW MET VAL ALA THR VAL 31.9588
387 5ISZ GLY ILE LEU GLY PHE VAL PHE THR LEU 31.9588
388 1OGA GLY ILE LEU GLY PHE VAL PHE THR LEU 31.9588
389 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 31.9588
Pocket No.: 2; Query (leader) PDB : 6GMN; Ligand: F4E; Similar sites found with APoc: 147
This union binding pocket(no: 2) in the query (biounit: 6gmn.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 5O0B 9FE None
2 1UO5 PIH None
3 2EW5 Y12 3.08642
4 3QCJ NX4 3.09278
5 1VLJ NAP 3.84615
6 2BHW NEX 4.32099
7 2Z6C FMN 4.65116
8 2YI0 YI0 4.80769
9 2AHR NAP 4.80769
10 5MBX SP5 4.93827
11 5MBX FAD 4.93827
12 5NTP 98E 5.15464
13 4ZAL FNR 5.15464
14 4ZAL 4LR 5.15464
15 3SP6 IL2 5.15464
16 3ET1 ET1 5.15464
17 2D5X L35 5.47945
18 4EOX 0S5 5.76923
19 1V1A ADP 5.76923
20 4RC8 STE 6.18557
21 1NU4 MLA 6.18557
22 4POJ 2VP 6.18557
23 6C1R EFD 6.18557
24 5TWO 7MV 6.18557
25 2OKL BB2 6.18557
26 3EBL GA4 6.18557
27 3O55 FAD 6.4
28 5WZU 7W3 6.50407
29 2B96 ANN 6.50407
30 4DK7 0KS 6.73077
31 6EOA FMN 6.73077
32 2HFK E4H 6.73077
33 5K52 OCD 6.73077
34 4E1N TQX 6.79012
35 3LLI FAD 6.79012
36 1Q1Y BB2 6.79012
37 4J26 EST 6.79012
38 3EE4 MYR 6.79012
39 3VC1 SAH 7.2165
40 2JLD AG1 7.40741
41 4DXD 9PC 7.69231
42 5UI2 EQ3 7.69231
43 1G55 SAH 7.69231
44 4H07 IPH 7.69231
45 2XN5 FUN 7.69231
46 3LTW HLZ 8.02469
47 5SYN 71T 8.02469
48 4ZGM 32M 8.19672
49 4WT2 3UD 8.24742
50 1ZDU P3A 8.24742
51 5M37 9SZ 8.24742
52 4MRT COA 8.24742
53 3GWL FAD 8.24742
54 3VZ3 NAP 8.64198
55 4GVS F4M 8.65385
56 2GJN FMN 8.65385
57 5CJH 522 8.65385
58 3D04 SAK 8.65385
59 3D9F FAD 9.27835
60 4JK3 NAD 9.27835
61 4Z87 GDP 9.61539
62 1NP7 FAD 9.61539
63 3GWT 066 9.87654
64 1XMU ROF 9.87654
65 1I2L DCS 10.3093
66 2Q8G AZX 10.3093
67 1MVN FMN 10.4938
68 5CB8 ADX 10.4938
69 3JRS A8S 10.4938
70 5DX1 SFG 10.5769
71 1IYE PGU 10.5769
72 2C6Q IMP 10.5769
73 2VAP GDP 10.5769
74 4YC9 4C1 10.5769
75 5WRJ A3P 11.1111
76 4MG8 27J 11.1111
77 5HYR EST 11.1111
78 5DXE EST 11.1111
79 4WQ2 3SU 11.3402
80 3VHE 42Q 11.3402
81 4HDK 13X 11.3402
82 1W96 S1A 11.3402
83 2PR5 FMN 11.3636
84 4URN NOV 11.5385
85 4URL XAM 11.5385
86 3ZS7 ATP 11.5385
87 5N9T 8QQ 12.3457
88 3SQP 3J8 12.3457
89 2QV6 GTP 12.3711
90 4XF6 INS 12.5
91 4XF6 LIP 12.5
92 4XF6 ADP 12.5
93 4NKW PLO 13.4615
94 3KMZ EQO 13.4615
95 6CR2 LFV 13.4615
96 1RQ2 CIT 13.5802
97 4C4A SAH 14.4231
98 6F68 GSH 14.4231
99 6F68 4EU 14.4231
100 6D55 FWA 14.4231
101 2XCM ADP 14.433
102 3R9C ECL 14.433
103 4RSL FAD 15.3846
104 2OFV 242 15.3846
105 4OIV XX9 15.4639
106 5LOF 70R 15.4639
107 2RHQ GAX 15.4639
108 5KOR GDP 15.4639
109 2VDY HCY 15.4639
110 3G4G D71 16.0494
111 3G58 988 16.0494
112 2FYU FDN 16.0494
113 2XSU PIE 16.3462
114 5IM3 DTP 16.3462
115 4PFC 2QX 16.3462
116 4M4Q 21A 16.4948
117 5J6A P46 16.6667
118 1D5Z ACE ALC ARG ALA ODA SER LEU NH2 17.284
119 1W5F G2P 17.3077
120 4A59 AMP 17.5258
121 2ZXG S23 18.2692
122 5B0I BOG 18.2692
123 3NB0 G6P 18.5185
124 4EES FMN 18.5567
125 1DNP FAD 18.5567
126 1WS1 BB2 18.5897
127 1ZEI CRS 18.8679
128 2LBD REA 20.1923
129 1FCZ 156 20.1923
130 2RH1 CLR 20.1923
131 1W2Y DUN 20.6186
132 4AG8 AXI 20.6186
133 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 21.6495
134 1X6V ADP 22.1154
135 1N6B DMZ 22.1154
136 2PSM BAM 23.0769
137 1MID LAP 24.1758
138 2VBQ BSJ 24.7423
139 5N5U 7N8 26.8041
140 1SR7 MOF 26.9231
141 4WO4 JLS 27.8846
142 1BW9 PPY 28.3951
143 1BXG HCI 28.3951
144 4E2J MOF 29.8077
145 5UFS 1TA 29.8077
146 5G57 6M5 31.9588
147 5MT9 SRO 47.619
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