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Receptor
PDB id Resolution Class Description Source Keywords
4DM8 2.3 Å EC: 2.3.1.48 CRYSTAL STRUCTURE OF RARB LBD IN COMPLEX WITH 9CIS RETINOIC HOMO SAPIENS NUCLEAR RECEPTOR RARB 9CIS RETINOIC ACID ALPHA HELICAL SATRANSCRIPTION FACTOR RETINOIC ACID TRANSCRIPTION-PROTEIN COMPLEX
Ref.: STRUCTURAL BASIS FOR A MOLECULAR ALLOSTERIC CONTROL MECHANISM OF COFACTOR BINDING TO NUCLEAR RECEPTORS. PROC.NATL.ACAD.SCI.USA V. 109 E588 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
REA A:501;
B:1501;
Valid;
Valid;
none;
none;
submit data
300.435 C20 H28 O2 CC1=C...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DM8 2.3 Å EC: 2.3.1.48 CRYSTAL STRUCTURE OF RARB LBD IN COMPLEX WITH 9CIS RETINOIC HOMO SAPIENS NUCLEAR RECEPTOR RARB 9CIS RETINOIC ACID ALPHA HELICAL SATRANSCRIPTION FACTOR RETINOIC ACID TRANSCRIPTION-PROTEIN COMPLEX
Ref.: STRUCTURAL BASIS FOR A MOLECULAR ALLOSTERIC CONTROL MECHANISM OF COFACTOR BINDING TO NUCLEAR RECEPTORS. PROC.NATL.ACAD.SCI.USA V. 109 E588 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 46 families.
1 4DM8 - REA C20 H28 O2 CC1=C(C(CC....
2 4DM6 - TTB C24 H28 O2 C/C(=Cc1cc....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 4DM8 - REA C20 H28 O2 CC1=C(C(CC....
2 4DM6 - TTB C24 H28 O2 C/C(=Cc1cc....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 3KMR - EQN C22 H25 N O3 CC1(CCC(c2....
2 4DM8 - REA C20 H28 O2 CC1=C(C(CC....
3 4DM6 - TTB C24 H28 O2 C/C(=Cc1cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: REA; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 REA 1 1
2 9CR 1 1
3 BCR 0.724138 0.730769
4 RET 0.704918 0.84
5 AZE 0.7 0.76
6 RTL 0.671875 0.758621
7 ECH 0.589041 0.724138
8 45D 0.410959 0.677419
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DM8; Ligand: REA; Similar sites found with APoc: 195
This union binding pocket(no: 1) in the query (biounit: 4dm8.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO5 PIH None
2 1UO4 PIH None
3 1JGS SAL None
4 6CS9 PIO None
5 5N8V KZZ None
6 4WG0 CHD None
7 5NNT DPV None
8 5LUN ARG 1.49813
9 3DCJ THH 1.86047
10 5IUY BOG 1.87266
11 6BR8 6OU 1.98413
12 2BHW NEX 2.15517
13 1MID LAP 2.1978
14 1HBK MYR 2.24719
15 1TV5 N8E 2.24719
16 5NM7 GLY 2.25564
17 1AUA BOG 2.62172
18 6D28 NEC 2.62172
19 2WTN FER 2.78884
20 5X3R 7Y3 2.92683
21 1UI0 URA 2.92683
22 1XF1 CIT 2.99625
23 4CCK OGA 2.99625
24 3W68 PBU 3.00752
25 5VRH OLB 3.06513
26 4MRP GSH 3.37079
27 3D9F FAD 3.37079
28 3D9F N6C 3.37079
29 3COW 52H 3.37079
30 5CQG 55C 3.74532
31 4RYV ZEA 3.87097
32 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 4.11985
33 6DIO CIT 4.11985
34 4DE3 DN8 4.18251
35 2CDC XYS 4.49438
36 4V1F BQ1 4.65116
37 4P3H 25G 4.66321
38 2YLD CMO 4.72441
39 3HP9 CF1 4.86891
40 4QGE 35O 4.86891
41 4WGF HX2 4.87805
42 4O4Z N2O 5.19481
43 5TI9 NFK 5.24345
44 4URG C2E 5.38922
45 3CYI ATP 5.45455
46 2D5X L35 5.47945
47 5Y02 HBX 5.60748
48 5Y02 MXN 5.60748
49 5AZC PGT 5.61798
50 4UBS DIF 5.61798
51 3HQ9 OXL 5.61798
52 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 6.27615
53 1NF8 BOG 6.28019
54 3A8H TAY 6.28019
55 2Q8G AZX 6.36704
56 2HZL PYR 6.74157
57 2QJY UQ2 6.74157
58 3RV5 DXC 6.74157
59 1RV1 IMZ 7.05882
60 3X27 TRP 7.11611
61 5UC4 83S 7.27273
62 1DTL BEP 7.45342
63 3NB0 G6P 7.86517
64 3TKY N7I 7.86517
65 6D5H FV7 7.86517
66 6D5J FV4 7.86517
67 6D5M FW4 7.86517
68 4URX FK1 7.86517
69 6D55 FWA 7.86517
70 6D5E FVG 7.86517
71 6D56 FVM 7.86517
72 6D59 FVJ 7.86517
73 6D5L FW7 7.86517
74 6D5G FVD 7.86517
75 6BVK EAV 7.86517
76 6BVM EBV 7.86517
77 4RW3 TDA 8
78 4G17 0VN 8
79 1XZ3 ICF 8.04598
80 2CB8 MYA 8.04598
81 5C9J DAO 8.08081
82 4OGQ 1O2 8.125
83 4OGQ 7PH 8.125
84 2YFB SIN 8.13953
85 1XVB 3BR 8.2397
86 5J32 IPM 8.2397
87 2BCG GER 8.25243
88 4IAE 1DX 8.46561
89 4UCC ZKW 8.58369
90 2OZ5 7XY 8.61423
91 3ZQE DXC 8.61423
92 1DCP HBI 8.65385
93 1WEI ADE 8.88889
94 4EXO PYR 8.90411
95 4QO5 NAG 8.98876
96 1OW4 2AN 9.30233
97 5OSW DIU 9.3633
98 1D6Z HY1 9.3633
99 6FS0 E4W 9.63303
100 3KP6 SAL 9.93377
101 3X1M COA 10.0629
102 3UP3 XCA 10.2881
103 3GYT DL4 11.0656
104 5OKL PAM 11.6105
105 1RL4 BL5 11.985
106 3KO0 TFP 12
107 3RMK BML 12.0482
108 1XXA ARG 12.8205
109 1Q7E MET 13.1086
110 5C1M OLC 13.8514
111 5G5W R8C 14.2322
112 1NHZ 486 14.2322
113 6BJO DUY 14.4
114 5I8F ML1 14.5455
115 4LSJ LSJ 14.7287
116 1M2Z DEX 14.786
117 1M2Z BOG 14.786
118 4P6X HCY 14.902
119 3TDC 0EU 14.9813
120 4P6W MOF 15.0794
121 4E2J MOF 15.6
122 3GN8 DEX 15.6627
123 5UFS 1TA 15.7258
124 5F1V 3VN 15.7303
125 3B99 U51 16
126 5X80 SAL 16.25
127 5UC1 486 17.1171
128 6CB2 OLC 19.1011
129 1YC4 43P 20
130 3AQT RCO 20
131 1JG0 DDT 20
132 4OAR 2S0 20.5993
133 1SR7 MOF 20.5993
134 5MWY YNU 21.7228
135 1Y75 NAG 22.0339
136 5L7G 6QE 22.0974
137 4UDB CV7 22.0974
138 3V49 PK0 22.1805
139 5DEY 59T 23.5955
140 2WOR 2AN 24
141 5Z84 CHD 24
142 5LX9 OLB 24
143 5W97 CHD 24
144 5ZCO CHD 24
145 5LWY OLB 24
146 3RY9 1CA 26.9663
147 4G86 BNT 28
148 1BRW URA 28
149 5KEW 6SB 28
150 2Q1H AS4 30
151 1T0S BML 30.2326
152 1YMT DR9 30.8943
153 1YP0 PEF 31.3808
154 3BJC WAN 32
155 5XJ7 87O 32
156 3SHZ 5CO 32
157 2XN5 FUN 32
158 4QJR PIZ 32.2097
159 1ZDT PEF 32.2097
160 2YVE MBT 36
161 1HG4 LPP 37.276
162 3GZ9 D32 37.4532
163 2P4Y C03 38.2022
164 3FUR Z12 38.2022
165 5TWO 7MV 38.2022
166 1YOK P6L 39.0625
167 4J26 EST 39.1667
168 5AAV GW5 40.0794
169 2E2R 2OH 40.1639
170 2O4J VD4 40.4494
171 3OKI OKI 40.7725
172 5UNJ RJW 40.8163
173 2QE4 JJ3 41.129
174 2R40 20E 41.1985
175 2R40 EPH 41.1985
176 3FS1 MYR 41.3043
177 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 41.3043
178 4Q0A 4OA 42.3221
179 5OCA 9QZ 44
180 1N46 PFA 45.3488
181 1YUC EPH 45.4902
182 1DB1 VDX 45.5598
183 5APK 76E 45.6604
184 3JZB 4HY 45.6929
185 3KFC 61X 45.8498
186 3L0E G58 46.2451
187 1N83 CLR 46.6667
188 5X8Q 82R 46.8992
189 4S15 4D8 47.2656
190 5NTW 98N 47.4708
191 5IXK 6EW 48.2456
192 1NQ7 ARL 48.7705
193 3VRV YSD 49.0637
194 5XPL 8C9 49.0637
195 5NTP 98E 49.5798
Pocket No.: 2; Query (leader) PDB : 4DM8; Ligand: REA; Similar sites found with APoc: 48
This union binding pocket(no: 2) in the query (biounit: 4dm8.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1UOU CMU 2.62172
2 2ZCQ B65 2.62172
3 5KBF CMP 2.99625
4 4IA6 EIC 2.99625
5 1OYJ GSH 3.0303
6 3ZUY TCH 3.09598
7 3GUZ PAF 3.40909
8 1MT1 AG2 3.53982
9 2J7T 274 3.74532
10 3ZVS MLI 3.75
11 1L0I PSR 3.84615
12 4B2Z P5S 4.11985
13 5NLM IOS 4.49438
14 4D4U FUC NDG GAL FUC 4.49438
15 6FBA D48 4.49438
16 3ROE THM 4.5283
17 3NJQ NJQ 4.66321
18 1R6N 434 4.73934
19 4BWL MN9 4.86891
20 4ETZ C2E 5.61798
21 5FPN KYD 5.99251
22 2NW9 FT6 5.99251
23 2CIX CEJ 6.02007
24 2OO0 XAP 6.36704
25 1GJW GLC 7.11611
26 3SDV 911 7.49064
27 2W9S TOP 8.07453
28 3GXO MQA 8.61423
29 3P2H MTA 8.61423
30 5NCB JZ3 8.61423
31 1A05 IPM 9.3633
32 1QFT HSM 10.8571
33 5TVI MYR 10.8696
34 5X13 HC4 11.7021
35 5BYK A3P 11.9691
36 5BYK OAQ 11.9691
37 6F9G PUT 11.985
38 5UC9 MYR 13.2743
39 3L1N PLM 13.8577
40 2AX9 BHM 16.7969
41 1ZEI CRS 18.8679
42 5CSD ACD 20.7547
43 5CX8 TG6 24
44 3R9V DXC 32
45 3D91 REM 36
46 1G2N EPH 37.1212
47 6AD9 KK4 38.2022
48 2VL1 GLY GLY 40
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