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 (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 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 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
22 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
23 2HAR - OCC C30 H50 O5 C[C@H](CCC....
24 3TKC - FMV C28 H40 O4 C[C@H](c1c....
25 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
26 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
70% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 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 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
23 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
24 2HAR - OCC C30 H50 O5 C[C@H](CCC....
25 3TKC - FMV C28 H40 O4 C[C@H](c1c....
26 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
27 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
28 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
29 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
30 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
2 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
3 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
4 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
5 1TXI - TX5 C27 H40 O3 C[C@H](CC#....
6 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
7 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
8 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
9 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
10 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
11 1PQ9 - BNS C6 H6 O3 S c1ccc(cc1)....
12 4RAK Ki = 14 nM 652 C28 H29 Cl N2 O3 S CC(C)(c1cc....
13 1PQ6 - 965 C33 H31 Cl F3 N O3 c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VDX; Similar ligands found: 42
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 VDZ 0.674157 1
8 YSV 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 EB1 0.6 0.928571
22 FMV 0.58 0.829787
23 TEY 0.576577 0.621212
24 ICJ 0.572816 0.97619
25 6VH 0.567308 0.833333
26 VD3 0.553191 0.853659
27 YS3 0.553191 0.97561
28 YS2 0.542553 0.909091
29 VDP 0.520661 0.634921
30 AKX 0.518519 0.930233
31 YSD 0.50505 0.928571
32 ZYD 0.50505 1
33 0CO 0.5 0.851064
34 COV 0.5 0.851064
35 VD1 0.463158 0.904762
36 H97 0.4375 0.851064
37 G72 0.4375 0.851064
38 YA1 0.435185 0.97619
39 YI3 0.425926 0.952381
40 YI4 0.405405 0.909091
41 TKA 0.403509 0.906977
42 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: 149
This union binding pocket(no: 1) in the query (biounit: 1db1.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WOR 2AN 0.0002873 0.53005 None
2 2BYC FMN 0.01003 0.42156 None
3 2HJ3 FAD 0.00743 0.41071 None
4 2QZT PLM 0.005325 0.40015 None
5 3O01 DXC 0.02789 0.40396 1.1583
6 3R9V DXC 0.03429 0.41254 1.5444
7 2J5S KTA 0.03602 0.40862 1.5444
8 3AQT RCO 0.03965 0.4082 1.63265
9 4IHL 1F5 0.01974 0.41448 1.70213
10 5UC9 MYR 0.02487 0.4191 1.76991
11 3B99 U51 0.003439 0.44855 1.9305
12 3WXL ADP 0.005842 0.44528 1.9305
13 5B25 4QJ 0.02261 0.40102 1.9305
14 1SBR VIB 0.02251 0.41967 2
15 3MBG FAD 0.003817 0.41126 2.15827
16 2HHP FLC 0.000545 0.46779 2.3166
17 3LXI CAM 0.04967 0.40035 2.3166
18 3O55 FAD 0.006093 0.40298 2.4
19 1A05 IPM 0.007922 0.44579 3.0888
20 1YC4 43P 0.004256 0.44395 3.0888
21 1Z4O GL1 0.02444 0.40265 3.16742
22 3RZ3 U94 0.01802 0.40914 3.27869
23 1ULE GLA GAL NAG 0.03222 0.41532 3.33333
24 1NF8 BOG 0.001066 0.49967 3.38164
25 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.004499 0.47699 3.4749
26 3GXO MQA 0.009537 0.43503 3.4749
27 4D1J DGJ 0.03875 0.40512 3.4749
28 3GWN FAD 0.0084 0.41144 3.50877
29 4UY1 TJM 0.03686 0.40052 3.81679
30 2VCN ISZ 0.009077 0.42758 3.861
31 4WGF HX2 0.03017 0.40261 3.90244
32 2PCU PHE ASN ARG PRO VAL 0.02641 0.41182 4.2471
33 4AQL TXC 0.01818 0.40236 4.2471
34 4V3I ASP LEU THR ARG PRO 0.02789 0.42015 4.28016
35 1PZ4 PLM 0.0161 0.40809 4.31034
36 1TV5 N8E 0.001378 0.48464 4.6332
37 1TV5 A26 0.0188 0.41557 4.6332
38 4N6H EJ4 0.03229 0.41119 4.6332
39 1XVB 3BR 0.008055 0.43438 4.70588
40 1XE7 GUN 0.04155 0.40061 4.92611
41 5B0I BOG 0.02373 0.40672 4.95627
42 5J32 IPM 0.007671 0.4471 5.01931
43 3B6C SDN 0.01844 0.42435 5.12821
44 4URN NOV 0.0302 0.41277 5.33333
45 3TDC 0EU 0.02109 0.41649 5.40541
46 3W5N RAM 0.02977 0.41204 5.40541
47 3NJQ NJQ 0.01343 0.43174 5.69948
48 4P3H 25G 0.007283 0.41749 5.69948
49 3BLI PYR 0.03805 0.41018 5.79151
50 1RL4 BRR 0.02947 0.41335 5.85106
51 1JR8 FAD 0.005939 0.41192 5.98291
52 5EW0 3C7 0.0321 0.41133 5.98291
53 3KFF XBT 0.03182 0.41154 6.17284
54 3KFF ZBT 0.03182 0.41154 6.17284
55 4UYG 73B 0.03509 0.41035 6.36943
56 5K53 STE 0.007186 0.41448 6.48855
57 4MRP GSH 0.00515 0.46075 6.56371
58 5LX9 OLB 0.001906 0.45662 6.56371
59 3EE4 MYR 0.009096 0.40685 6.56371
60 1BGV GLU 0.01414 0.43164 7.33591
61 4RW3 SHV 0.02332 0.41972 7.33591
62 3HP9 CF1 0.03316 0.41457 7.33591
63 4HBM 0Y7 0.01679 0.40088 7.5
64 1VPD TLA 0.02322 0.41866 7.72201
65 4L77 CNL 0.04195 0.40501 7.72201
66 5LWY OLB 0.007715 0.42711 8.41121
67 5G5W R8C 0.0001428 0.46554 8.49421
68 1NHZ 486 0.001322 0.43997 8.49421
69 4LSJ LSJ 0.00007531 0.49804 8.52713
70 1M2Z DEX 0.0001693 0.48717 8.56031
71 1M2Z BOG 0.01519 0.44394 8.56031
72 3BQD DAY 0.000399 0.46635 8.62745
73 4P6W MOF 0.0001668 0.47858 8.73016
74 3DBX PLM 0.004521 0.44265 8.88031
75 2YLD CMO 0.00716 0.45252 9.44882
76 1DZK PRZ 0.01508 0.40944 10.1911
77 2A9G ARG 0.02985 0.40525 10.4247
78 1XI9 PLP 0.0396 0.40252 10.8108
79 2Q1H AS4 0.0001666 0.49223 11.2
80 1SR7 MOF 0.000222 0.44458 11.583
81 4OAR 2S0 0.00005469 0.50907 11.6279
82 4E2J MOF 0.0001625 0.47906 12.4
83 5OCA 9QZ 0.02292 0.43336 12.4424
84 3GN8 DEX 0.000185 0.48545 12.4498
85 5UFS 1TA 0.0004614 0.45961 12.5
86 1YYE 196 0.00004165 0.53717 12.7413
87 2I0G I0G 0.001519 0.42815 12.8405
88 3UP3 XCA 0.0005092 0.45399 13.1687
89 1U3R 338 0.00004516 0.52356 13.6929
90 3OLL EST 0.00002768 0.53944 13.75
91 4J26 EST 0.0000697 0.53258 13.75
92 2YJD YJD 0.00008472 0.51639 13.75
93 2CB8 MYA 0.03409 0.41271 13.7931
94 4I67 G G G RPC 0.03153 0.40402 13.7931
95 1S8G DAO 0.03009 0.40153 14.876
96 3V49 PK0 0.00005961 0.48891 15.444
97 2AX9 BHM 0.0002655 0.41089 15.625
98 1ECM TSA 0.01673 0.42225 16.5138
99 5DXE EST 0.00008035 0.40169 19.6911
100 5HYR EST 0.00009018 0.40048 21.3178
101 4MGA 27L 0.00008147 0.54841 21.5686
102 4MGB XDH 0.0000139 0.54732 21.5686
103 4MGD 27N 0.00002864 0.54506 21.5686
104 4MG9 27K 0.0003853 0.51419 21.5686
105 4MG7 27H 0.0001034 0.50683 21.5686
106 4MG8 27J 0.0001987 0.50426 21.5686
107 3UUD EST 0.00006415 0.52807 21.9123
108 3UUA 0CZ 0.0002086 0.51503 21.9123
109 3UU7 2OH 0.005153 0.45404 21.9123
110 1H0A I3P 0.04027 0.40795 23.4177
111 4P6X HCY 0.0002282 0.40534 23.5294
112 3RY9 1CA 0.0001315 0.50199 26
113 5HCV 60R 0.000083 0.50099 26.07
114 4UDB CV7 0.0001635 0.47077 26.2548
115 5L7G 6QE 0.00004671 0.43419 26.2548
116 2A3I C0R 0.0001047 0.49177 26.4822
117 5APJ 76E 0.000005291 0.48818 31.2741
118 5APK 76E 0.00005901 0.44781 31.2741
119 5NTW 98N 0.00001378 0.47805 31.9066
120 5IXK 6EW 0.0004155 0.46978 35.5263
121 3SP6 IL2 0.00003937 0.52075 35.9073
122 3ET1 ET1 0.00006986 0.51475 35.9073
123 3KDU NKS 0.0002201 0.45889 35.9073
124 2P54 735 0.0003691 0.45253 35.9073
125 2NPA MMB 0.002003 0.43568 35.9073
126 1K7L 544 0.003243 0.41414 35.9073
127 4ZOM 4Q3 0.00002449 0.51593 36
128 1XIU REA 0.002854 0.43987 36.5217
129 4J24 EST 0.0000711 0.53215 36.8421
130 2XN5 FUN 0.01631 0.41873 37.1429
131 3FUR Z12 0.00001056 0.50764 37.4517
132 5TWO 7MV 0.0002174 0.48233 37.4517
133 2PRG BRL 0.000365 0.48139 37.4517
134 3G9E RO7 0.00002395 0.47197 37.4517
135 1RDT 570 0.0006299 0.44653 37.4517
136 1RDT L79 0.001906 0.44024 37.4517
137 3H0A 9RA 0.00249 0.43875 37.4517
138 4S15 4D8 0.00002326 0.52037 39.0625
139 4DK7 0KS 0.00000007051 0.64578 42.915
140 3OKI OKI 0.0001009 0.42418 43.7768
141 5ICK FEZ 0.00000961 0.54863 45.4148
142 3RUU 37G 0.000001776 0.53674 45.4148
143 4DM8 REA 0.00005908 0.49793 45.5598
144 3JZB 4HY 0.00006069 0.47651 45.5598
145 4OIV XX9 0.0004392 0.40899 46.4602
146 2R40 20E 0.000004864 0.53395 47.1042
147 3KMR EQN 0.000109 0.50062 47.7444
148 3KMZ EQO 0.00001956 0.50004 47.7444
149 1N46 PFA 0.000006878 0.52286 48.062
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