Receptor
PDB id Resolution Class Description Source Keywords
4AWJ 2.5 Å NON-ENZYME: TRANSCRIPT_TRANSLATE PVHL:ELOB:ELOC COMPLEX, IN COMPLEX WITH CAPPED HYDROXYPROLIN HOMO SAPIENS TRANSCRIPTION E3 UBIQUITIN LIGASE TUMOR SUPRESSOR
Ref.: DISSECTING FRAGMENT-BASED LEAD DISCOVERY AT THE VON LINDAU PROTEIN:HYPOXIA INDUCIBLE FACTOR 1ALPHA PROT PROTEIN INTERFACE. CHEM.BIOL. V. 19 1300 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:1104;
B:1113;
C:1202;
F:1207;
I:1207;
L:1207;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
ACY F:1206;
Invalid;
none;
submit data
60.052 C2 H4 O2 CC(=O...
GOL J:1104;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
V6F C:1201;
F:1205;
I:1206;
L:1206;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd ~ 10000 uM
186.208 C8 H14 N2 O3 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5NVX 2.2 Å NON-ENZYME: TRANSCRIPT_TRANSLATE PVHL:ELOB:ELOC IN COMPLEX WITH (2S,4R)-1-((S)-2-(1- FLUOROCYCLOPROPANECARBOXAMIDO)-3,3-DIMETHYLBUTANOYL)-4-HYDR( 4-METHYLTHIAZOL-5-YL)BENZYL)PYRROLIDINE-2-CARBOXAMIDE (LIG HOMO SAPIENS PROTEIN COMPLEX UBIQUITIN LIGASE HYPOXIA INDUCIBLE FACTOR
Ref.: GROUP-BASED OPTIMIZATION OF POTENT AND CELL-ACTIVE INHIBITORS OF THE VON HIPPEL-LINDAU (VHL) E3 UBIQUI LIGASE: STRUCTURE-ACTIVITY RELATIONSHIPS LEADING TO CHEMICAL PROBE (2S,4R)-1-((S)-2-(1-CYANOCYCLOPROPANECARBOXAMIDO)-3 3-DIMETHYLBUTANOYL)-4-HYDROX
Members (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 308 families.
1 5NVX Kd = 44 nM 4YY C26 H33 F N4 O4 S Cc1c(scn1)....
2 4W9J Kd = 0.588 uM 3JH C30 H43 N5 O5 S Cc1c(scn1)....
3 6GFZ Kd = 3080 nM EXE C24 H31 F N4 O4 S Cc1c(scn1)....
4 5NW1 Kd = 210 nM 9BH C27 H36 N4 O4 S Cc1c(scn1)....
5 5LLI Kd = 90 nM 6Z3 C27 H33 N5 O4 S Cc1c(scn1)....
6 5NVV Kd = 105 nM 9BT C24 H32 N4 O5 S Cc1c(scn1)....
7 4W9L Kd = 9.52 uM 3JJ C30 H43 N5 O5 S Cc1c(scn1)....
8 4W9C Kd = 22.2 uM 3JG C21 H27 N3 O4 CC(C)(C)CC....
9 5NW0 Kd = 128 nM 9BK C28 H37 N5 O5 S Cc1c(scn1)....
10 5NVW Kd = 132 nM 9BW C26 H34 N4 O4 S Cc1c(scn1)....
11 4W9D Kd = 10.2 uM 3JK C22 H29 N3 O4 Cc1c(ocn1)....
12 4AWJ Kd ~ 10000 uM V6F C8 H14 N2 O3 CC(=O)N1C[....
13 6FMJ Kd = 0.76 uM DV5 C21 H26 N4 O3 S2 Cc1c(scn1)....
14 4W9I Kd = 1.1 uM 3JS C23 H28 N4 O5 S Cc1c(scn1)....
15 5NW2 Kd = 232 nM 9B8 C26 H34 N4 O5 S Cc1c(scn1)....
16 4BKT Kd = 240 uM QD0 C12 H17 N3 O4 Cc1cc(on1)....
17 4W9K Kd = 0.291 uM 3JO C33 H41 N5 O5 S Cc1c(scn1)....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 5NVX Kd = 44 nM 4YY C26 H33 F N4 O4 S Cc1c(scn1)....
2 4W9J Kd = 0.588 uM 3JH C30 H43 N5 O5 S Cc1c(scn1)....
3 6GFZ Kd = 3080 nM EXE C24 H31 F N4 O4 S Cc1c(scn1)....
4 5NW1 Kd = 210 nM 9BH C27 H36 N4 O4 S Cc1c(scn1)....
5 5LLI Kd = 90 nM 6Z3 C27 H33 N5 O4 S Cc1c(scn1)....
6 5NVV Kd = 105 nM 9BT C24 H32 N4 O5 S Cc1c(scn1)....
7 4W9L Kd = 9.52 uM 3JJ C30 H43 N5 O5 S Cc1c(scn1)....
8 4W9C Kd = 22.2 uM 3JG C21 H27 N3 O4 CC(C)(C)CC....
9 5NW0 Kd = 128 nM 9BK C28 H37 N5 O5 S Cc1c(scn1)....
10 5NVW Kd = 132 nM 9BW C26 H34 N4 O4 S Cc1c(scn1)....
11 4W9D Kd = 10.2 uM 3JK C22 H29 N3 O4 Cc1c(ocn1)....
12 4AWJ Kd ~ 10000 uM V6F C8 H14 N2 O3 CC(=O)N1C[....
13 6FMJ Kd = 0.76 uM DV5 C21 H26 N4 O3 S2 Cc1c(scn1)....
14 4W9I Kd = 1.1 uM 3JS C23 H28 N4 O5 S Cc1c(scn1)....
15 5NW2 Kd = 232 nM 9B8 C26 H34 N4 O5 S Cc1c(scn1)....
16 4BKT Kd = 240 uM QD0 C12 H17 N3 O4 Cc1cc(on1)....
17 4W9K Kd = 0.291 uM 3JO C33 H41 N5 O5 S Cc1c(scn1)....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 families.
1 5NVX Kd = 44 nM 4YY C26 H33 F N4 O4 S Cc1c(scn1)....
2 4W9J Kd = 0.588 uM 3JH C30 H43 N5 O5 S Cc1c(scn1)....
3 6GFZ Kd = 3080 nM EXE C24 H31 F N4 O4 S Cc1c(scn1)....
4 5NW1 Kd = 210 nM 9BH C27 H36 N4 O4 S Cc1c(scn1)....
5 5LLI Kd = 90 nM 6Z3 C27 H33 N5 O4 S Cc1c(scn1)....
6 5NVV Kd = 105 nM 9BT C24 H32 N4 O5 S Cc1c(scn1)....
7 4W9L Kd = 9.52 uM 3JJ C30 H43 N5 O5 S Cc1c(scn1)....
8 4W9C Kd = 22.2 uM 3JG C21 H27 N3 O4 CC(C)(C)CC....
9 5NW0 Kd = 128 nM 9BK C28 H37 N5 O5 S Cc1c(scn1)....
10 5NVW Kd = 132 nM 9BW C26 H34 N4 O4 S Cc1c(scn1)....
11 4W9D Kd = 10.2 uM 3JK C22 H29 N3 O4 Cc1c(ocn1)....
12 4AWJ Kd ~ 10000 uM V6F C8 H14 N2 O3 CC(=O)N1C[....
13 6FMJ Kd = 0.76 uM DV5 C21 H26 N4 O3 S2 Cc1c(scn1)....
14 4W9I Kd = 1.1 uM 3JS C23 H28 N4 O5 S Cc1c(scn1)....
15 5NW2 Kd = 232 nM 9B8 C26 H34 N4 O5 S Cc1c(scn1)....
16 4BKT Kd = 240 uM QD0 C12 H17 N3 O4 Cc1cc(on1)....
17 4W9K Kd = 0.291 uM 3JO C33 H41 N5 O5 S Cc1c(scn1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: V6F; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 V6F 1 1
2 QD0 0.428571 0.783333
Similar Ligands (3D)
Ligand no: 1; Ligand: V6F; Similar ligands found: 333
No: Ligand Similarity coefficient
1 PHT 0.9392
2 GLY PRO 0.9369
3 AIN 0.9339
4 NTM 0.9335
5 KLW 0.9307
6 PRZ 0.9272
7 FLC 0.9203
8 ENL 0.9180
9 329 0.9173
10 0GY 0.9165
11 URC 0.9150
12 KIB 0.9141
13 CDV 0.9126
14 S3B 0.9125
15 GV9 0.9119
16 PXL 0.9107
17 CIT 0.9103
18 60Q 0.9077
19 ICT 0.9071
20 NFQ 0.9064
21 8XQ 0.9061
22 8TX 0.9058
23 AH8 0.9057
24 QAT 0.9053
25 7ZE 0.9048
26 GZ8 0.9044
27 YQA 0.9034
28 GTZ 0.9023
29 DOR 0.9019
30 GLC 0.9019
31 NCD 0.9013
32 GLY LEU 0.9006
33 GLY ASP 0.9003
34 GUN 0.8995
35 HJP 0.8991
36 9MG 0.8991
37 ORO 0.8985
38 GAL 0.8984
39 M3S 0.8983
40 GM7 0.8979
41 2MN 0.8979
42 TRA 0.8979
43 EKN 0.8979
44 ALA PRO 0.8978
45 9DG 0.8978
46 AME 0.8978
47 SLC 0.8977
48 XAN 0.8977
49 KIA 0.8971
50 SR4 0.8969
51 II6 0.8969
52 3MG 0.8969
53 BGC 0.8968
54 ZZ8 0.8967
55 GTL 0.8965
56 MBG 0.8965
57 Z5P 0.8959
58 1AL 0.8959
59 AKH 0.8956
60 QAS 0.8948
61 X8Z 0.8940
62 Q6T 0.8939
63 DBJ 0.8938
64 LT8 0.8938
65 GCS 0.8934
66 S76 0.8932
67 ASC 0.8930
68 G3F 0.8927
69 JKZ 0.8925
70 34D 0.8925
71 IJZ 0.8923
72 OXC 0.8922
73 V55 0.8920
74 FOT 0.8920
75 F69 0.8920
76 6XI 0.8917
77 4ME 0.8916
78 HNQ 0.8912
79 8VE 0.8912
80 LSA 0.8911
81 CCB 0.8910
82 1U1 0.8910
83 B55 0.8909
84 HA7 0.8909
85 GJS 0.8908
86 GYE 0.8905
87 42C 0.8905
88 7VS 0.8904
89 5WX 0.8903
90 TRC 0.8901
91 D1X 0.8899
92 2CG 0.8897
93 XQK 0.8896
94 F12 0.8891
95 4TE 0.8889
96 S7B 0.8888
97 5WY 0.8888
98 61O 0.8887
99 QPR 0.8887
100 YSO 0.8884
101 C2U 0.8883
102 3S4 0.8881
103 SHG 0.8880
104 8S0 0.8879
105 MFU 0.8875
106 VNL 0.8872
107 5RG 0.8871
108 K3Q 0.8870
109 IPZ 0.8869
110 HH5 0.8869
111 HLD 0.8867
112 UEG 0.8867
113 N7P 0.8867
114 DQA 0.8861
115 7A2 0.8859
116 3MA 0.8854
117 AOR 0.8852
118 EV0 0.8852
119 FA6 0.8851
120 YH7 0.8850
121 SXS 0.8850
122 2A7 0.8849
123 QM1 0.8847
124 2ZQ 0.8846
125 K2P 0.8842
126 AUD 0.8839
127 OTD 0.8838
128 1X7 0.8838
129 Q88 0.8838
130 MMA 0.8835
131 ECG 0.8834
132 39U 0.8833
133 UAN 0.8832
134 AN0 0.8830
135 SF6 0.8830
136 N8P 0.8830
137 BOA 0.8828
138 1XM 0.8827
139 AZG 0.8823
140 MVL 0.8823
141 ALA LEU 0.8822
142 8WQ 0.8822
143 AZA 0.8821
144 J01 0.8820
145 5JQ 0.8817
146 CKX 0.8816
147 3C2 0.8815
148 3IT 0.8815
149 GOG 0.8813
150 75K 0.8813
151 0GZ 0.8812
152 DNC 0.8811
153 YIO 0.8811
154 VOH 0.8811
155 LGC 0.8810
156 512 0.8809
157 SF9 0.8807
158 BDF 0.8807
159 ZWZ 0.8807
160 692 0.8806
161 FA3 0.8805
162 8IG 0.8802
163 0CU 0.8802
164 12M 0.8802
165 7WR 0.8802
166 FPK 0.8801
167 6CS 0.8799
168 49N 0.8799
169 AS3 0.8798
170 141 0.8798
171 FRU 0.8798
172 M1E 0.8794
173 GCO 0.8793
174 NZ3 0.8792
175 BMA 0.8792
176 GTC 0.8791
177 2H5 0.8790
178 5JL 0.8790
179 NSG 0.8790
180 GNL 0.8790
181 XAZ 0.8789
182 AW5 0.8789
183 8GK 0.8788
184 JR2 0.8786
185 D07 0.8780
186 M1H 0.8780
187 P4B 0.8780
188 9KH 0.8779
189 M0Q 0.8778
190 DX4 0.8777
191 3C1 0.8776
192 2FG 0.8774
193 AX3 0.8772
194 12B 0.8769
195 VPR 0.8768
196 GOX 0.8767
197 ADK 0.8764
198 TVP 0.8762
199 BTY 0.8761
200 FBG 0.8756
201 NGT 0.8755
202 1FF 0.8754
203 KFH 0.8751
204 GT0 0.8750
205 MAN 0.8750
206 M0W 0.8749
207 GTR 0.8744
208 A2F 0.8744
209 149 0.8743
210 KG1 0.8743
211 O2A 0.8742
212 GIV 0.8740
213 7D2 0.8739
214 7NI 0.8737
215 BDP 0.8735
216 IGA 0.8735
217 SHA 0.8732
218 DHK 0.8732
219 TWO 0.8731
220 290 0.8731
221 A13 0.8730
222 2AL 0.8729
223 293 0.8729
224 Q24 0.8729
225 G4D 0.8727
226 BCP 0.8719
227 GLA 0.8719
228 CFP 0.8717
229 6AP 0.8717
230 X09 0.8716
231 BK9 0.8714
232 PDC 0.8714
233 6LW 0.8710
234 OEM 0.8710
235 40H 0.8710
236 NZ2 0.8709
237 PCV 0.8707
238 GCB 0.8707
239 GIO 0.8707
240 NGO 0.8706
241 HLZ 0.8704
242 NIG 0.8704
243 F0J 0.8703
244 PA1 0.8703
245 4XV 0.8702
246 UNC 0.8701
247 ZZ3 0.8697
248 LFR 0.8693
249 K3Y 0.8692
250 1GN 0.8692
251 SER PRO 0.8690
252 XQG 0.8689
253 MIC 0.8688
254 CKU 0.8687
255 TFU 0.8687
256 R9S 0.8686
257 2TQ 0.8685
258 HHT 0.8681
259 AZ8 0.8677
260 5HY 0.8677
261 DIE 0.8676
262 FBU 0.8676
263 IPM 0.8674
264 FP1 0.8672
265 790 0.8671
266 SWA 0.8671
267 8VN 0.8667
268 8EZ 0.8663
269 I3A 0.8662
270 256 0.8658
271 GDE 0.8657
272 9PY 0.8657
273 QIC 0.8656
274 EMZ 0.8656
275 AMG 0.8656
276 PE0 0.8655
277 NID 0.8648
278 ES0 0.8646
279 DIU 0.8646
280 261 0.8642
281 1Z8 0.8641
282 EVA 0.8641
283 ISD 0.8639
284 SKM 0.8639
285 GLG 0.8638
286 JTH 0.8636
287 GCU 0.8634
288 FYU 0.8632
289 KT7 0.8631
290 M3Q 0.8626
291 AM1 0.8624
292 AHR 0.8624
293 X6X 0.8622
294 210 0.8619
295 49O 0.8609
296 AHD 0.8607
297 3DM 0.8606
298 KDO 0.8604
299 DBH 0.8599
300 52C 0.8597
301 6VD 0.8597
302 23J 0.8596
303 C9E 0.8596
304 CWM 0.8593
305 6W6 0.8592
306 G5V 0.8591
307 MEW 0.8586
308 4MU 0.8584
309 M5K 0.8583
310 FUL 0.8583
311 KP6 0.8581
312 EUG 0.8578
313 4M4 0.8578
314 2PG 0.8575
315 AQO 0.8574
316 2J9 0.8574
317 AJ2 0.8571
318 2D0 0.8569
319 4CS 0.8567
320 2LP 0.8564
321 ZB1 0.8556
322 ARW 0.8556
323 57O 0.8552
324 NVU 0.8550
325 NGW 0.8542
326 FDK 0.8540
327 3AL 0.8534
328 NLA 0.8533
329 FH2 0.8533
330 GXL 0.8531
331 44V 0.8529
332 MS9 0.8525
333 5PX 0.8518
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5NVX; Ligand: 4YY; 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: 5nvx.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5NVX; Ligand: 4YY; 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: 5nvx.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5NVX; Ligand: 4YY; 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: 5nvx.bio4) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5NVX; Ligand: 4YY; 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: 5nvx.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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