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Receptor
PDB id Resolution Class Description Source Keywords
2O4J 1.74 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF RAT VITAMIN D RECEPTOR LIGAND BINDING D COMPLEXED WITH VITIII 17-20Z AND THE NR2 BOX OF DRIP 205 RATTUS NORVEGICUS NUCLEAR RECEPTOR-LIGAND COMPLEX HORMONE-GROWTH FACTOR RECEPCOMPLEX
Ref.: NEW ANALOGS OF 2-METHYLENE-19-NOR-(20S)-1,25-DIHYDROXYVITAMIN D(3) CONFORMATIONALLY RESTRICTED SIDE CHAINS: EVALUATION BIOLOGICAL ACTIVITY AND STRUCTURAL DETERMINATION OF VDR-BOUND CONFORMATIONS. ARCH.BIOCHEM.BIOPHYS. V. 460 161 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
VD4 A:500;
Valid;
none;
Ki = 0.08 nM
414.621 C27 H42 O3 C/C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2O4J 1.74 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF RAT VITAMIN D RECEPTOR LIGAND BINDING D COMPLEXED WITH VITIII 17-20Z AND THE NR2 BOX OF DRIP 205 RATTUS NORVEGICUS NUCLEAR RECEPTOR-LIGAND COMPLEX HORMONE-GROWTH FACTOR RECEPCOMPLEX
Ref.: NEW ANALOGS OF 2-METHYLENE-19-NOR-(20S)-1,25-DIHYDROXYVITAMIN D(3) CONFORMATIONALLY RESTRICTED SIDE CHAINS: EVALUATION BIOLOGICAL ACTIVITY AND STRUCTURAL DETERMINATION OF VDR-BOUND CONFORMATIONS. ARCH.BIOCHEM.BIOPHYS. V. 460 161 2007
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 286 families.
1 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
2 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
3 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
4 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
5 2O4R Kd = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
6 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
70% Homology Family (54)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 2ZMI ic50 = 3 nM TT2 C35 H52 O3 C[C@@H](C=....
2 3VT6 - 5YI C28 H44 O4 S CCC(CC)(CS....
3 3W0I - O11 C26 H38 O5 CCC(CC)(c1....
4 3VT9 - YI4 C31 H50 O4 C[C@H](CCC....
5 3VT5 - YI2 C28 H44 O4 S CCC(CC)(CS....
6 2ZLA - VDB C28 H46 O5 S CCC(CC)(CS....
7 2ZLC - VDX C27 H44 O3 C[C@H](CCC....
8 3VT7 - VDX C27 H44 O3 C[C@H](CCC....
9 2ZFX - YR3 C28 H42 O5 CCC(CC)(c1....
10 3VJT ic50 = 4.1 uM 10R C17 H42 B10 O4 [BH]1234[B....
11 3WT5 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
12 5XPM ic50 = 23 nM 8C0 C36 H54 O4 CCCC[C@@H]....
13 4YNK - YW2 C34 H44 O3 C[C@]12CCC....
14 5B41 - YSV C27 H44 O3 C[C@H](CCC....
15 3W0H - W12 C28 H42 O5 CCCC(CCC)(....
16 3W0G - W07 C24 H34 O5 CC(C)(C)[C....
17 3VTB ic50 = 0.5 nM TKA C35 H50 O3 C[C@H](CC#....
18 5XZF ic50 = 0.24 nM 8J0 C35 H50 O3 C[C@H](CC#....
19 5B5B ic50 = 0.43 nM AKX C39 H52 O3 C[C@H](CCC....
20 5XPO ic50 = 84 nM 8BL C31 H42 O4 C[C@H](CCC....
21 5ZWI ic50 = 2.3 nM 9KX C27 H38 O3 C/C=C/C=C/....
22 3VT8 - YI3 C30 H52 O3 CCCC[C@@H]....
23 3W0J - T08 C26 H38 O5 Cc1cc(ccc1....
24 3VT4 - 5YI C28 H44 O4 S CCC(CC)(CS....
25 3VJS ic50 = 0.64 uM 10S C17 H42 B10 O4 [BH]1234[B....
26 3W5T - LHP C27 H44 O4 CCC(=O)O[C....
27 3VRU ic50 = 0.1 nM YS3 C26 H42 O3 C[C@H](CCC....
28 3AUN - YR4 C29 H44 O5 CCC(CC)(c1....
29 2ZMH - NYA C34 H50 O3 C[C@H](C=C....
30 5AWJ ic50 = 0.21 nM YSL C30 H50 O3 CCCCCC[C@@....
31 3W5R - LOA C26 H42 O4 C[C@H](CCC....
32 2ZL9 - VDA C28 H46 O5 S CCC(CC)(CS....
33 5XZH ic50 = 3.13 nM 8J3 C35 H50 O3 C[C@H](CC#....
34 3VRW ic50 = 0.41 nM YS5 C32 H54 O3 CCCC[C@@H]....
35 3VT3 - VDX C27 H44 O3 C[C@H](CCC....
36 3VRT ic50 = 2.7 nM YS2 C24 H38 O3 C[C@H](CCC....
37 3VTC ic50 = 13 nM TK3 C36 H52 O3 C[C@H](CC#....
38 3AFR - ICJ C31 H52 O3 CCCC[C@@H]....
39 3WT6 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
40 5XPN ic50 = 102 nM 9RO C32 H46 O4 C[C@H](CCC....
41 5ZWH ic50 = 1.9 nM 9N9 C27 H36 O3 C/C=C/C#CC....
42 2ZXN - JC1 C28 H46 O3 CCCC[C@@H]....
43 3A2H - TEJ C27 H38 O4 C[C@@H](C[....
44 3W5P - 4OA C24 H40 O3 C[C@H](CCC....
45 3WT7 ic50 = 1.79 nM YA2 C32 H54 O3 CCCC[C@H](....
46 3VRV ic50 = 0.029 nM YSD C28 H46 O3 CCC(CC)(CC....
47 3W5Q - 3KL C24 H38 O3 C[C@H](CCC....
48 2ZMJ ic50 = 30 nM MI4 C36 H54 O3 C[C@@H](C=....
49 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
50 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
51 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
52 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
53 2O4R Kd = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
54 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
50% Homology Family (54)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 174 families.
1 2ZMI ic50 = 3 nM TT2 C35 H52 O3 C[C@@H](C=....
2 3VT6 - 5YI C28 H44 O4 S CCC(CC)(CS....
3 3W0I - O11 C26 H38 O5 CCC(CC)(c1....
4 3VT9 - YI4 C31 H50 O4 C[C@H](CCC....
5 3VT5 - YI2 C28 H44 O4 S CCC(CC)(CS....
6 2ZLA - VDB C28 H46 O5 S CCC(CC)(CS....
7 2ZLC - VDX C27 H44 O3 C[C@H](CCC....
8 3VT7 - VDX C27 H44 O3 C[C@H](CCC....
9 2ZFX - YR3 C28 H42 O5 CCC(CC)(c1....
10 3VJT ic50 = 4.1 uM 10R C17 H42 B10 O4 [BH]1234[B....
11 3WT5 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
12 5XPM ic50 = 23 nM 8C0 C36 H54 O4 CCCC[C@@H]....
13 4YNK - YW2 C34 H44 O3 C[C@]12CCC....
14 5B41 - YSV C27 H44 O3 C[C@H](CCC....
15 3W0H - W12 C28 H42 O5 CCCC(CCC)(....
16 3W0G - W07 C24 H34 O5 CC(C)(C)[C....
17 3VTB ic50 = 0.5 nM TKA C35 H50 O3 C[C@H](CC#....
18 5XZF ic50 = 0.24 nM 8J0 C35 H50 O3 C[C@H](CC#....
19 5B5B ic50 = 0.43 nM AKX C39 H52 O3 C[C@H](CCC....
20 5XPO ic50 = 84 nM 8BL C31 H42 O4 C[C@H](CCC....
21 5ZWI ic50 = 2.3 nM 9KX C27 H38 O3 C/C=C/C=C/....
22 3VT8 - YI3 C30 H52 O3 CCCC[C@@H]....
23 3W0J - T08 C26 H38 O5 Cc1cc(ccc1....
24 3VT4 - 5YI C28 H44 O4 S CCC(CC)(CS....
25 3VJS ic50 = 0.64 uM 10S C17 H42 B10 O4 [BH]1234[B....
26 3W5T - LHP C27 H44 O4 CCC(=O)O[C....
27 3VRU ic50 = 0.1 nM YS3 C26 H42 O3 C[C@H](CCC....
28 3AUN - YR4 C29 H44 O5 CCC(CC)(c1....
29 2ZMH - NYA C34 H50 O3 C[C@H](C=C....
30 5AWJ ic50 = 0.21 nM YSL C30 H50 O3 CCCCCC[C@@....
31 3W5R - LOA C26 H42 O4 C[C@H](CCC....
32 2ZL9 - VDA C28 H46 O5 S CCC(CC)(CS....
33 5XZH ic50 = 3.13 nM 8J3 C35 H50 O3 C[C@H](CC#....
34 3VRW ic50 = 0.41 nM YS5 C32 H54 O3 CCCC[C@@H]....
35 3VT3 - VDX C27 H44 O3 C[C@H](CCC....
36 3VRT ic50 = 2.7 nM YS2 C24 H38 O3 C[C@H](CCC....
37 3VTC ic50 = 13 nM TK3 C36 H52 O3 C[C@H](CC#....
38 3AFR - ICJ C31 H52 O3 CCCC[C@@H]....
39 3WT6 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
40 5XPN ic50 = 102 nM 9RO C32 H46 O4 C[C@H](CCC....
41 5ZWH ic50 = 1.9 nM 9N9 C27 H36 O3 C/C=C/C#CC....
42 2ZXN - JC1 C28 H46 O3 CCCC[C@@H]....
43 3A2H - TEJ C27 H38 O4 C[C@@H](C[....
44 3W5P - 4OA C24 H40 O3 C[C@H](CCC....
45 3WT7 ic50 = 1.79 nM YA2 C32 H54 O3 CCCC[C@H](....
46 3VRV ic50 = 0.029 nM YSD C28 H46 O3 CCC(CC)(CC....
47 3W5Q - 3KL C24 H38 O3 C[C@H](CCC....
48 2ZMJ ic50 = 30 nM MI4 C36 H54 O3 C[C@@H](C=....
49 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
50 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
51 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
52 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
53 2O4R Kd = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
54 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VD4; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 VD4 1 1
2 VD5 1 1
3 YSV 0.459184 1
4 VDZ 0.459184 1
5 YS3 0.443299 0.97561
6 YA1 0.432692 0.97619
7 YSD 0.415842 0.928571
8 VD1 0.414894 0.904762
9 YS2 0.40404 0.909091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2O4J; Ligand: VD4; Similar sites found with APoc: 189
This union binding pocket(no: 1) in the query (biounit: 2o4j.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 2VKL MLT None
2 1UO5 PIH None
3 2QZT PLM None
4 4WG0 CHD None
5 2WOR 2AN None
6 3KPE TM3 None
7 5IUY BOG 1.36986
8 5X3R 7Y3 1.46341
9 6A0S NDP 1.71233
10 5J32 IPM 2.05479
11 3GXO MQA 2.05479
12 3NB0 G6P 2.05479
13 3JQ9 AX1 2.08333
14 2BHW NEX 2.15517
15 2HZL PYR 2.39726
16 2PYW SR1 2.39726
17 2CW6 3HG 2.39726
18 2WHL MAN BMA BMA 2.39726
19 5EO8 TFU 2.39726
20 4D52 GIV 2.39726
21 4D52 GXL 2.39726
22 5NC9 8SZ 2.42915
23 3AQT RCO 2.44898
24 4RYV ZEA 2.58065
25 5FPN KYD 2.73973
26 4MRP GSH 2.73973
27 3B6C SDN 2.73973
28 1ITU CIL 2.73973
29 3B99 U51 2.73973
30 4K10 NI9 2.73973
31 1YRO UDP 2.7972
32 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.08219
33 3RMK BML 3.08219
34 1ZED PNP 3.08219
35 1UAS GLA 3.08219
36 4EKQ NPO 3.20856
37 1JAY F42 3.30189
38 4WGF HX2 3.41463
39 3ZQE DXC 3.42466
40 2WPF FAD 3.42466
41 2WPF WPF 3.42466
42 1J78 OLA 3.42466
43 5EEH P9P 3.76712
44 4M3P HCS 3.76712
45 3KIV ACA 3.79747
46 2GBB CIT 3.84615
47 3HP9 CF1 3.94191
48 1ULE GLA GAL NAG 4
49 1VEM GLC GLC 4.10959
50 5OCM 9RH 4.12371
51 1PZ4 PLM 4.31034
52 3V78 ET 4.32692
53 1ONI BEZ 4.34783
54 5EB3 UEG 4.40252
55 5CXI 5TW 4.4335
56 3CEV ARG 4.45205
57 5XJ7 87O 4.47761
58 4QGE 35O 4.50281
59 2YLD CMO 4.72441
60 1T0S BML 4.79452
61 4DNJ ANN 4.79452
62 5ZQ4 AMP 4.79452
63 1UI0 URA 4.87805
64 3KFF ZBT 4.93827
65 3KFF XBT 4.93827
66 2D5X L35 4.96454
67 6CB2 OLC 5.13699
68 4IA6 EIC 5.13699
69 4GVF NAG 5.13699
70 4GVF NDG 5.13699
71 5AZC PGT 5.13699
72 5HCN DAO 5.36398
73 4P3H 25G 5.69948
74 1NF8 BOG 5.7971
75 5OKL PAM 5.82192
76 5WP4 PC 5.82192
77 4DE3 DN8 6.08365
78 4DDY DN6 6.08365
79 4X1B MLI 6.16438
80 4MA6 28E 6.36943
81 1RL4 BRR 6.38298
82 4DOL PLM 6.45161
83 4XCP PLM 6.47059
84 5LX6 78P 6.80628
85 3G4Q MCH 6.84932
86 6DIO CIT 6.84932
87 2OHV NHL 6.84932
88 4UYF 73B 7.14286
89 6BVI EC4 7.18563
90 6BVL EBY 7.18563
91 6BVM EBV 7.18563
92 6BVK EAV 7.18563
93 6BVJ EAS 7.18563
94 3Q8G PEE 7.5
95 2OZ5 7XY 7.53425
96 6BR8 6OU 7.53968
97 6BR8 PGV 7.53968
98 4OGQ 7PH 7.82123
99 2CB8 MYA 8.04598
100 2Q8G AZX 8.21918
101 2BCG GER 8.25243
102 1A05 IPM 8.56164
103 3BQD DAY 8.62745
104 2VDY HCY 8.90411
105 2ZUV NDG 8.90411
106 4C6H HE2 8.93471
107 2QQC AG2 9.43396
108 2OMN IPH 9.58904
109 1MT1 AG2 9.61539
110 3KP6 SAL 9.93377
111 5I8T LAC 10.0559
112 2BYC FMN 10.219
113 2X5F PLP 10.274
114 3BKR PLM 11.1111
115 1DTL BEP 11.1801
116 1KYZ FER 11.3014
117 1R6N 434 11.3744
118 1YYE 196 11.5672
119 2I0G I0G 12.0623
120 2YVE MBT 12.4324
121 1U3R 338 12.8631
122 3UP3 XCA 13.1687
123 1HBK MYR 13.4831
124 3TL1 JRO 13.8365
125 1ECM TSA 15.5963
126 2IDO TMP 18.0723
127 2Y69 CHD 20.6349
128 2BJ4 OHT 22.2222
129 5ZCO CHD 27.6596
130 5Z84 CHD 27.6596
131 5W97 CHD 27.6596
132 1PZL MYR 29.1139
133 5NI5 8YB 29.1667
134 3FS1 MYR 30
135 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 30
136 3GYT DL4 30.3279
137 4WPF 3SN 31.8182
138 3ET1 ET1 31.9588
139 2E2R 2OH 32.377
140 2XN3 ID8 32.5
141 5X8Q 82R 32.5581
142 3KDU NKS 33.574
143 4POJ 2VP 34.1991
144 4M8E 29V 34.1991
145 2P54 735 34.8315
146 3ET3 ET1 34.9315
147 3GZ9 D32 34.9442
148 6AD9 KK4 35.5401
149 3T03 3T0 35.9155
150 1N4H REA 36.2934
151 2HFP NSI 36.5248
152 2P4Y C03 36.8231
153 1HG4 LPP 36.9176
154 2XN5 FUN 37.1429
155 1YOK P6L 37.5
156 3H0A 9RA 37.8676
157 1FM9 9CR 37.8676
158 1FM9 570 37.8676
159 3G9E RO7 38.0074
160 2PRG BRL 38.0074
161 3W68 PBU 38.4615
162 1TV5 A26 38.4615
163 1TV5 N8E 38.4615
164 1N83 CLR 38.5185
165 1NQ7 ARL 38.5246
166 5UNJ RJW 39.1837
167 5AAV GW5 39.2857
168 4DM8 REA 40.4494
169 1XAP TTB 40.4494
170 5HCV 60R 40.4669
171 2A3I C0R 41.1067
172 3BEJ MUF 44.5378
173 3OKI OKI 45.0644
174 3DCT 064 45.1064
175 4DK7 0KS 45.3441
176 5UV1 0FV 46.1538
177 4RW3 SHV 46.1538
178 3RUU 37G 46.2882
179 5ICK FEZ 46.2882
180 2QZO KN1 46.5116
181 2QA8 GEN 46.5116
182 3IPQ 965 46.9965
183 4OIV XX9 47.3451
184 3KMR EQN 47.3684
185 3UUA 0CZ 47.8088
186 3UU7 2OH 47.8088
187 3UUD EST 47.8088
188 2LBD REA 47.9401
189 2QE4 JJ3 47.9839
Pocket No.: 2; Query (leader) PDB : 2O4J; Ligand: VD4; 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: 2o4j.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2O4J; Ligand: VD4; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 2o4j.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 4CQB MLI 2.05479
2 4D1J DGJ 2.05479
3 3V1S 0LH 2.39726
4 3U1T MLI 3.08219
5 4OUE IPT 5.13699
6 1XZ3 ICF 6.32184
7 6CED EYA 6.54206
8 1MID LAP 6.59341
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