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Receptor
PDB id Resolution Class Description Source Keywords
1DB1 1.8 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMP VITAMIN D HOMO SAPIENS COMPLEX GENE REGULATION
Ref.: THE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR V BOUND TO ITS NATURAL LIGAND. MOL.CELL V. 5 173 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
VDX A:428;
Valid;
none;
Kd = 0.55 nM
416.636 C27 H44 O3 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DB1 1.8 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMP VITAMIN D HOMO SAPIENS COMPLEX GENE REGULATION
Ref.: THE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR V BOUND TO ITS NATURAL LIGAND. MOL.CELL V. 5 173 2000
Members (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 291 families.
1 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
2 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
3 2HAS - C3O C30 H50 O4 CCCO[C@H]1....
4 1S0Z - EB1 C30 H46 O3 CCC(CC)(C=....
5 3AZ1 - DS2 C27 H38 O5 CCC(CC)(c1....
6 1IE9 - VDX C27 H44 O3 C[C@H](CCC....
7 2HAM - C33 C30 H50 O3 CCC[C@H]1[....
8 2HB8 - MVD C28 H46 O3 C[C@H]1[C@....
9 3CS4 - COV C28 H44 O4 C[C@]12CCC....
10 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
11 3M7R - VDX C27 H44 O3 C[C@H](CCC....
12 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
13 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
14 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
15 1TXI - TX5 C27 H40 O3 C[C@H](CC#....
16 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
17 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
18 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
19 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
20 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
21 5YT2 - 90O C29 H48 O4 C[C@H](CCC....
22 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
23 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
24 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
25 2HAR - OCC C30 H50 O5 C[C@H](CCC....
26 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
27 3TKC - FMV C28 H40 O4 C[C@H](c1c....
28 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
29 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
30 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
31 5YSY - 90L C29 H48 O4 C[C@H](CCC....
70% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 families.
1 4Q0A Kd = 0.33 uM 4OA C24 H40 O3 C[C@H](CCC....
2 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
3 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
4 2HAS - C3O C30 H50 O4 CCCO[C@H]1....
5 1S0Z - EB1 C30 H46 O3 CCC(CC)(C=....
6 3AZ1 - DS2 C27 H38 O5 CCC(CC)(c1....
7 1IE9 - VDX C27 H44 O3 C[C@H](CCC....
8 2HAM - C33 C30 H50 O3 CCC[C@H]1[....
9 2HB8 - MVD C28 H46 O3 C[C@H]1[C@....
10 3CS4 - COV C28 H44 O4 C[C@]12CCC....
11 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
12 3M7R - VDX C27 H44 O3 C[C@H](CCC....
13 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
14 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
15 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
16 1TXI - TX5 C27 H40 O3 C[C@H](CC#....
17 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
18 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
19 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
20 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
21 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
22 5YT2 - 90O C29 H48 O4 C[C@H](CCC....
23 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
24 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
25 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
26 2HAR - OCC C30 H50 O5 C[C@H](CCC....
27 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
28 3TKC - FMV C28 H40 O4 C[C@H](c1c....
29 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
30 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
31 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
32 5YSY - 90L C29 H48 O4 C[C@H](CCC....
50% Homology Family (42)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 4Q0A Kd = 0.33 uM 4OA C24 H40 O3 C[C@H](CCC....
2 4X1F Ki = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
3 5M24 - 9CR C20 H28 O2 CC1=C(C(CC....
4 1FCY Kd = 3 nM 564 C26 H26 O3 CC1(CCC(c2....
5 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
6 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
7 2HAS - C3O C30 H50 O4 CCCO[C@H]1....
8 1S0Z - EB1 C30 H46 O3 CCC(CC)(C=....
9 3AZ1 - DS2 C27 H38 O5 CCC(CC)(c1....
10 1IE9 - VDX C27 H44 O3 C[C@H](CCC....
11 2HAM - C33 C30 H50 O3 CCC[C@H]1[....
12 2HB8 - MVD C28 H46 O3 C[C@H]1[C@....
13 3CS4 - COV C28 H44 O4 C[C@]12CCC....
14 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
15 3M7R - VDX C27 H44 O3 C[C@H](CCC....
16 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
17 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
18 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
19 1TXI - TX5 C27 H40 O3 C[C@H](CC#....
20 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
21 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
22 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
23 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
24 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
25 5YT2 - 90O C29 H48 O4 C[C@H](CCC....
26 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
27 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
28 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
29 2HAR - OCC C30 H50 O5 C[C@H](CCC....
30 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
31 3TKC - FMV C28 H40 O4 C[C@H](c1c....
32 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
33 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
34 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
35 5YSY - 90L C29 H48 O4 C[C@H](CCC....
36 1PQ9 - BNS C6 H6 O3 S c1ccc(cc1)....
37 4RAK Ki = 14 nM 652 C28 H29 Cl N2 O3 S CC(C)(c1cc....
38 1UPV - 444 C17 H12 F9 N O3 S c1ccc(cc1)....
39 1PQ6 - 965 C33 H31 Cl F3 N O3 c1ccc(cc1)....
40 1UPW - 444 C17 H12 F9 N O3 S c1ccc(cc1)....
41 5JY3 Ki = 12 nM 6OX C29 H28 Cl2 F2 N2 O4 S CC(C)(c1cn....
42 3KFC ic50 = 2.8 nM 61X C23 H16 F3 N O3 S CS(=O)(=O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VDX; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 VDX 1 1
2 BIV 0.758621 1
3 MVD 0.714286 1
4 VDY 0.712644 0.926829
5 M7E 0.693878 0.672414
6 TX5 0.692308 0.952381
7 YSV 0.674157 1
8 VDZ 0.674157 1
9 C33 0.659794 0.97619
10 ZNE 0.656863 0.754717
11 VD2 0.655556 0.97561
12 O1C 0.653061 0.931818
13 C3O 0.646465 0.891304
14 7ZU 0.641304 0.951219
15 OCC 0.633663 0.87234
16 TEJ 0.628866 0.847826
17 JC1 0.625 0.888889
18 MC9 0.623656 0.904762
19 91W 0.614583 0.866667
20 KH1 0.61 0.888889
21 8J3 0.607843 0.906977
22 8J0 0.607843 0.906977
23 EB1 0.6 0.928571
24 FMV 0.58 0.829787
25 TEY 0.576577 0.621212
26 ICJ 0.572816 0.97619
27 6VH 0.567308 0.833333
28 YS3 0.553191 0.97561
29 VD3 0.553191 0.853659
30 YS2 0.542553 0.909091
31 VDP 0.520661 0.634921
32 AKX 0.518519 0.930233
33 YSD 0.50505 0.928571
34 ZYD 0.50505 1
35 COV 0.5 0.851064
36 0CO 0.5 0.851064
37 VD1 0.463158 0.904762
38 8BL 0.446429 0.909091
39 9RO 0.442478 0.888889
40 8BO 0.442478 0.888889
41 H97 0.4375 0.851064
42 G72 0.4375 0.851064
43 YA1 0.435185 0.97619
44 YI3 0.425926 0.952381
45 AYT 0.419048 0.926829
46 YI4 0.405405 0.909091
47 TKA 0.403509 0.906977
48 TK3 0.401709 0.906977
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1DB1; Ligand: VDX; Similar sites found with APoc: 246
This union binding pocket(no: 1) in the query (biounit: 1db1.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
1 2WOR 2AN None
2 3KPE TM3 None
3 1HBK MYR None
4 5UC4 83S None
5 2BYC FMN None
6 3ZO7 K6H None
7 4F4S EFO None
8 2HJ3 FAD None
9 6BOC EU7 None
10 3GWL FAD None
11 5TVI MYR None
12 6EIZ FOH None
13 2QZT PLM None
14 3O01 DXC 1.1583
15 5IUY BOG 1.5444
16 3R9V DXC 1.5444
17 2J5S KTA 1.5444
18 3AQT RCO 1.63265
19 4IHL 1F5 1.70213
20 5UC9 MYR 1.76991
21 3B99 U51 1.9305
22 3WXL ADP 1.9305
23 1HK8 DGT 1.9305
24 5B25 4QJ 1.9305
25 1SBR VIB 2
26 2BHW NEX 2.15517
27 3MBG FAD 2.15827
28 4DE3 DN8 2.3166
29 2HHP FLC 2.3166
30 4DE2 DN3 2.3166
31 3CEV ARG 2.3166
32 4DDY DN6 2.3166
33 1H5R THM 2.3166
34 3U6W KIV 2.3166
35 1K7W AS1 2.3166
36 3LXI CAM 2.3166
37 1OQC FAD 2.4
38 3O55 FAD 2.4
39 2RH1 CLR 2.7027
40 6FK6 DOK 2.7027
41 1GNI OLA 2.7027
42 5K52 OCD 2.7027
43 5N26 73M 2.74725
44 1A05 IPM 3.0888
45 1YC4 43P 3.0888
46 4G86 BNT 3.0888
47 1Z4O GL1 3.16742
48 3RZ3 U94 3.27869
49 1NF8 BOG 3.38164
50 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.4749
51 3GXO MQA 3.4749
52 5OSW DIU 3.4749
53 5AZC PGT 3.4749
54 4D1J DGJ 3.4749
55 3GWN FAD 3.50877
56 3E3U NVC 3.5533
57 5FPN KYD 3.861
58 5JCJ 6JM 3.861
59 6D28 NEC 3.861
60 4CME KTZ 3.861
61 3N75 G4P 3.861
62 4WGF HX2 3.90244
63 2PCU PHE ASN ARG PRO VAL 4.2471
64 4AQL TXC 4.2471
65 4V3I ASP LEU THR ARG PRO 4.28016
66 1PZ4 PLM 4.31034
67 5XNA SHV 4.34783
68 5EB3 UEG 4.40252
69 5XJ7 87O 4.47761
70 1TV5 N8E 4.6332
71 5U5G 7VD 4.6332
72 1TV5 A26 4.6332
73 4N6H EJ4 4.6332
74 3NB0 G6P 4.6332
75 4YSX E23 4.6332
76 1XVB 3BR 4.70588
77 5C1M 4VO 4.8
78 5B0I BOG 4.95627
79 5J32 IPM 5.01931
80 3B6C SDN 5.12821
81 4RYV ZEA 5.16129
82 4URN NOV 5.33333
83 3TDC 0EU 5.40541
84 3W5N RAM 5.40541
85 3NJQ NJQ 5.69948
86 4P3H 25G 5.69948
87 1ZED PNP 5.79151
88 2Q8G AZX 5.79151
89 3W54 RNB 5.79151
90 4V1F BQ1 5.81395
91 1RL4 BRR 5.85106
92 2HFN FMN 5.88235
93 6FS0 E4W 5.9633
94 1JR8 FAD 5.98291
95 5EW0 3C7 5.98291
96 6D5H FV7 5.98802
97 6BVM EBV 5.98802
98 6BVK EAV 5.98802
99 6BVI EC4 5.98802
100 6D5J FV4 5.98802
101 6BVJ EAS 5.98802
102 6BVL EBY 5.98802
103 6D59 FVJ 5.98802
104 6D56 FVM 5.98802
105 4OGQ 7PH 6.04651
106 4OGQ UMQ 6.04651
107 3KFF ZBT 6.17284
108 3KFF XBT 6.17284
109 4UYG 73B 6.36943
110 5K53 STE 6.48855
111 5OKL PAM 6.56371
112 4MRP GSH 6.56371
113 5LX9 OLB 6.56371
114 3EE4 MYR 6.56371
115 1DTL BEP 6.8323
116 5EEH P9P 6.91489
117 6DIO CIT 6.94981
118 1FX8 BOG 6.94981
119 6BR9 6OU 6.94981
120 4UHL VFV 6.94981
121 6BR8 6OU 7.14286
122 6BR8 PGV 7.14286
123 4XB4 45D 7.23684
124 2BCG GER 7.33591
125 5UV1 0FV 7.33591
126 1BGV GLU 7.33591
127 4RW3 SHV 7.33591
128 4GVF NDG 7.33591
129 4GVF NAG 7.33591
130 3HP9 CF1 7.33591
131 4HBM 0Y7 7.5
132 5ZQ4 AMP 7.69231
133 6CB2 OLC 7.72201
134 4QGE 35O 8.10811
135 5I8T LAC 8.37989
136 5LWY OLB 8.41121
137 5G5W R8C 8.49421
138 2OZ5 7XY 8.49421
139 1NHZ 486 8.49421
140 3TKY N7I 8.49421
141 4LSJ LSJ 8.52713
142 4RC8 STE 8.55856
143 1M2Z DEX 8.56031
144 1M2Z BOG 8.56031
145 3BQD DAY 8.62745
146 4P6W MOF 8.73016
147 3DBX PLM 8.88031
148 2YLD CMO 9.44882
149 5UC1 486 9.90991
150 1DZK PRZ 10.1911
151 2A9G ARG 10.4247
152 1XI9 PLP 10.8108
153 5NM7 GLY 11.1969
154 2Q1H AS4 11.2
155 5Z84 CHD 11.5646
156 1SR7 MOF 11.583
157 5CX6 CDP 11.583
158 4OAR 2S0 11.6279
159 4E2J MOF 12.4
160 5OCA 9QZ 12.4424
161 3GN8 DEX 12.4498
162 5UFS 1TA 12.5
163 1YYE 196 12.7413
164 2I0G I0G 12.8405
165 5N8V KZZ 13.0435
166 3UP3 XCA 13.1687
167 5TDF ADE 13.5135
168 1U3R 338 13.6929
169 3OLL EST 13.75
170 4J26 EST 13.75
171 2YJD YJD 13.75
172 2CB8 MYA 13.7931
173 4I67 G G G RPC 13.7931
174 1S8G DAO 14.876
175 3V49 PK0 15.444
176 2AX9 BHM 15.625
177 3ER9 3AT 15.8301
178 4QXB OGA 16.1765
179 1ECM TSA 16.5138
180 2Y69 CHD 17.5
181 5WGD EST 19.6911
182 5WGQ EST 19.6911
183 5DX3 EST 19.6911
184 5DXE EST 19.6911
185 5DXG EST 19.6911
186 5HYR EST 21.3178
187 4MGD 27N 21.5686
188 4MGA 27L 21.5686
189 4TUZ 36J 21.5686
190 4MG7 27H 21.5686
191 4MG8 27J 21.5686
192 4MGB XDH 21.5686
193 4MG9 27K 21.5686
194 3UUD EST 21.9123
195 3UUA 0CZ 21.9123
196 4TV1 36M 21.9123
197 3UU7 2OH 21.9123
198 1H0A I3P 23.4177
199 4P6X HCY 23.5294
200 5MWY YNU 25.8687
201 3RY9 1CA 26
202 5HCV 60R 26.07
203 5L7G 6QE 26.2548
204 4UDB CV7 26.2548
205 2A3I C0R 26.4822
206 1BWO LPC 28.8889
207 6ESN BWE 31.2741
208 5APK 76E 31.2741
209 5NTW 98N 31.9066
210 2XN3 ID8 32.5
211 5NTP 98E 34.4538
212 5IXK 6EW 35.5263
213 3SP6 IL2 35.9073
214 3ET1 ET1 35.9073
215 3KDU NKS 35.9073
216 2P54 735 35.9073
217 2NPA MMB 35.9073
218 3FEI CTM 35.9073
219 1K7L 544 35.9073
220 4J24 EST 36.8421
221 2XN5 FUN 37.1429
222 5TWO 7MV 37.4517
223 2PRG BRL 37.4517
224 3G9E RO7 37.4517
225 1RDT 570 37.4517
226 1RDT L79 37.4517
227 3H0A 9RA 37.4517
228 3FUR Z12 37.4517
229 2HFP NSI 37.4517
230 4REF 3N0 38.2812
231 4S15 4D8 39.0625
232 4DK7 0KS 42.915
233 3OKI OKI 43.7768
234 5ICK FEZ 45.4148
235 3RUU 37G 45.4148
236 3JZB 4HY 45.5598
237 4DM8 REA 45.5598
238 6A5Y 9R0 46.0526
239 6A5Y 9CR 46.0526
240 4OIV XX9 46.4602
241 2R40 20E 47.1042
242 3KMR EQN 47.7444
243 3KMZ EQO 47.7444
244 1N46 PFA 48.062
245 6FX0 E9T 48.2625
246 5K13 6Q7 49.187
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