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Receptor
PDB id Resolution Class Description Source Keywords
1XAP 2.1 Å NON-ENZYME: TRANSCRIPT_TRANSLATE STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE RETINOIC ACID BETA HOMO SAPIENS NUCLEAR RECEPTOR LIGAND BINDING DOMAIN RETINOIC ACID RECEPTTNPB TRANSCRIPTION
Ref.: RATIONAL DESIGN OF RAR-SELECTIVE LIGANDS REVEALED B CRYSTAL STRUCTURE EMBO REP. V. 5 877 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TTB A:1;
Valid;
none;
Kd = 2.5 nM
348.478 C24 H28 O2 C/C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1XAP 2.1 Å NON-ENZYME: TRANSCRIPT_TRANSLATE STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE RETINOIC ACID BETA HOMO SAPIENS NUCLEAR RECEPTOR LIGAND BINDING DOMAIN RETINOIC ACID RECEPTTNPB TRANSCRIPTION
Ref.: RATIONAL DESIGN OF RAR-SELECTIVE LIGANDS REVEALED B CRYSTAL STRUCTURE EMBO REP. V. 5 877 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 291 families.
1 1XAP Kd = 2.5 nM TTB C24 H28 O2 C/C(=Cc1cc....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 families.
1 1FCZ Kd = 0.6 nM 156 C24 H26 O3 CC1(CCC(c2....
2 1FD0 Kd ~ 4 nM 254 C26 H27 N O3 CC1(CCC(c2....
3 1FCX Kd = 64 nM 184 C26 H28 O3 CC1(CCC(c2....
4 1EXA - 394 C23 H26 F N O4 CC1(CCC(c2....
5 1EXX - 961 C23 H26 F N O4 CC1(CCC(c2....
6 3LBD - REA C20 H28 O2 CC1=C(C(CC....
7 5M24 - 9CR C20 H28 O2 CC1=C(C(CC....
8 1FCY Kd = 3 nM 564 C26 H26 O3 CC1(CCC(c2....
9 5K13 Ki = 1.8 nM 6Q7 C27 H26 N2 O4 S CC(C)(C)c1....
10 1XAP Kd = 2.5 nM TTB C24 H28 O2 C/C(=Cc1cc....
11 2LBD - REA C20 H28 O2 CC1=C(C(CC....
12 4LBD - 961 C23 H26 F N O4 CC1(CCC(c2....
50% Homology Family (53)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 174 families.
1 3JZB ic50 ~ 0.1 nM 4HY C14 H9 I3 O4 c1cc(c(cc1....
2 4LNW - T3 C15 H12 I3 N O4 c1cc(c(cc1....
3 2H79 - T3 C15 H12 I3 N O4 c1cc(c(cc1....
4 3HZF - B72 C20 H24 O4 Cc1cc(cc(c....
5 1NAV - IH5 C17 H16 Cl2 O4 CC(C)c1cc(....
6 4LNX - T44 C15 H11 I4 N O4 c1c(cc(c(c....
7 2H77 - T3 C15 H12 I3 N O4 c1cc(c(cc1....
8 3ET0 - GLC C6 H12 O6 C([C@@H]1[....
9 5Y2T - 8LX C24 H24 N4 O5 S CN(CCOc1cc....
10 4E4Q - RRH C24 H24 O3 CC(C)c1ccc....
11 1KNU - YPA C25 H25 N O4 CCO[C@@H](....
12 2Q8S ic50 = 0.185 uM L92 C26 H26 N2 O3 Cc1c(nc(o1....
13 2YFE Ki = 0.236 uM YFE C21 H24 O4 CC(=CCc1c(....
14 4EM9 - KNA C9 H18 O2 CCCCCCCCC(....
15 2Q6S - PLB C18 H11 Cl2 N3 O4 c1cnc(nc1)....
16 3AN4 - M7R C37 H43 N O4 CCCOc1ccc(....
17 3PBA - ZXG C15 H12 Br4 O5 S CC(C)(c1cc....
18 3ADV Kd = 933 uM SRO C10 H12 N2 O c1cc2c(cc1....
19 6ENQ - BJB C19 H15 Cl N2 O4 S2 c1cc2c(cc1....
20 6C1I ic50 = 85 nM EEY C12 H8 Cl N3 O3 c1cc(c(cc1....
21 2Q5S - NZA C22 H15 Cl2 N O2 S c1ccc(cc1)....
22 5F9B - 5VN C30 H48 O5 C[C@]12CC[....
23 2I4P - DRH C27 H36 N2 O4 CCCCCCC[N@....
24 5LSG Kd = 4 uM QZQ C30 H46 O3 CC(=C)[C@@....
25 5TTO - 7KK C21 H11 Br Cl2 F2 N2 O3 S c1ccc2c(c1....
26 5HZC - 65W C20 H18 O3 CC(C)(C(=O....
27 3IA6 ic50 = 0.003 uM UNT C24 H24 N4 O3 Cc1c(nc(o1....
28 3ADX - IMN C19 H16 Cl N O4 Cc1c(c2cc(....
29 6F2L - AXY C27 H22 O3 c1ccc(cc1)....
30 3HOD - ZZH C22 H20 O3 c1ccc(cc1)....
31 6AVI - KNA C9 H18 O2 CCCCCCCCC(....
32 2I4Z - DRH C27 H36 N2 O4 CCCCCCC[N@....
33 5U44 - 7SV C29 H30 F N O4 c1ccc(c(c1....
34 3TKM Kd = 22 nM GW0 C21 H17 F4 N O3 S2 Cc1cc(ccc1....
35 5U41 - 7UG C31 H31 N O4 S c1ccc(cc1)....
36 5U42 - 7SM C30 H33 N O5 COc1cccc(c....
37 5U3U - 7TV C29 H33 N O5 c1ccc(c(c1....
38 3GZ9 Ki = 0.004 uM D32 C27 H23 F3 O5 S Cc1c(c(ccc....
39 5U46 - 7T1 C21 H18 F3 N O3 S2 Cc1cc(ccc1....
40 5U3R - 7V1 C27 H31 N O5 CC(C)N(Cc1....
41 3ET2 - ET1 C19 H19 N O6 S COc1ccc(cc....
42 5U43 - 7SS C30 H33 N O5 COc1ccc(cc....
43 2B50 - VCA C18 H34 O2 CCCCCCC=CC....
44 3PEQ ic50 = 32 nM 3EQ C30 H31 N O5 S2 CCCC[N@@](....
45 3VI8 - 13M C30 H27 N O4 CC[C@@H](C....
46 2ZNN - S44 C32 H41 N O4 CCCOc1ccc(....
47 5HYK - 65W C20 H18 O3 CC(C)(C(=O....
48 3LBD - REA C20 H28 O2 CC1=C(C(CC....
49 1NQ2 - 4HY C14 H9 I3 O4 c1cc(c(cc1....
50 1XZX Kd = 0.06 nM T3 C15 H12 I3 N O4 c1cc(c(cc1....
51 3JZC ic50 ~ 1 nM 4HY C14 H9 I3 O4 c1cc(c(cc1....
52 1NQ0 - 4HY C14 H9 I3 O4 c1cc(c(cc1....
53 1XAP Kd = 2.5 nM TTB C24 H28 O2 C/C(=Cc1cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TTB; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 TTB 1 1
2 UV8 0.606061 0.84375
3 156 0.587302 0.833333
4 R13 0.521739 0.962963
5 EQN 0.515152 0.615385
6 564 0.470588 0.8
7 254 0.464789 0.615385
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1XAP; Ligand: TTB; Similar sites found with APoc: 194
This union binding pocket(no: 1) in the query (biounit: 1xap.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 6CS9 PIO None
2 4GCZ FMN None
3 1IYB 5GP 1.44231
4 2VSU V55 1.49813
5 1SBR VIB 1.5
6 5IUY BOG 1.87266
7 6BR8 PGV 1.98413
8 5XJ7 87O 1.99005
9 1MID LAP 2.1978
10 1NE7 16G 2.24719
11 5CX8 TG6 2.24719
12 5NM7 GLY 2.25564
13 2JAP J01 2.42915
14 3IA4 MTX 2.46914
15 3JQM GTP 2.54777
16 3V1S 0LH 2.62172
17 4XNV BUR 2.62172
18 2ZCQ B65 2.62172
19 4URN NOV 2.66667
20 2WTN FER 2.78884
21 4GV4 MEJ 2.99625
22 5OHJ 9VE 2.99625
23 4IA6 EIC 2.99625
24 3KYQ DPV 3.01508
25 5VRH OLB 3.06513
26 2Z6D FMN 3.07692
27 5LX9 OLB 3.37079
28 4MRP GSH 3.37079
29 5N87 N66 3.37079
30 4CCW VKC 3.37079
31 3GUZ PAF 3.40909
32 1N13 AG2 3.53982
33 1MT1 AG2 3.53982
34 4WBD ADP 3.74532
35 1L0I PSR 3.84615
36 1RQH PYR 4.11985
37 4DE3 DN8 4.18251
38 2QCX PF1 4.18251
39 1TO9 HMH 4.23077
40 4BFW ZVW 4.40252
41 6FBA D48 4.49438
42 2CDC XYS 4.49438
43 4V1F BQ1 4.65116
44 3NJQ NJQ 4.66321
45 2YLD CMO 4.72441
46 3HP9 CF1 4.86891
47 5TDF ADE 4.86891
48 4QGE 35O 4.86891
49 4E90 7RG 4.86891
50 4WGF HX2 4.87805
51 3KO0 TFP 4.9505
52 2F2G HMH 4.97738
53 4O4Z N2O 5.19481
54 2D5X L35 5.47945
55 2V0U FMN 5.47945
56 5DJT FMN 5.51724
57 5DJU FMN 5.51724
58 5Y02 HBX 5.60748
59 3O01 DXC 5.61798
60 4ETZ C2E 5.61798
61 4UBS DIF 5.61798
62 5AZC PGT 5.61798
63 5KAU RHQ 6.06061
64 5B25 4QJ 6.36704
65 2Q8G AZX 6.36704
66 2HZL PYR 6.74157
67 3RV5 DXC 6.74157
68 5MDH MAK 6.74157
69 2QJY UQ2 6.74157
70 5CX6 CDP 7.11611
71 1DTL BEP 7.45342
72 5LWY OLB 7.56302
73 5DKK FMN 7.58621
74 4RW3 TDA 7.86517
75 3NB0 G6P 7.86517
76 6BVK EAV 7.86517
77 6BVM EBV 7.86517
78 5A2Z GTP 7.86517
79 3TKY N7I 7.86517
80 1XZ3 ICF 8.04598
81 2W9S TOP 8.07453
82 3G08 FEE 8.08081
83 4OGQ 7PH 8.125
84 3AQT RCO 8.16327
85 5J32 IPM 8.2397
86 4UCC ZKW 8.58369
87 3NV6 CAM 8.61423
88 2OZ5 7XY 8.61423
89 5NCB JZ3 8.61423
90 3P2H MTA 8.61423
91 3GXO MQA 8.61423
92 4EXO PYR 8.90411
93 1N8V BDD 8.92857
94 4QO5 NAG 8.98876
95 1A05 IPM 9.3633
96 5OSW DIU 9.3633
97 3X1M COA 10.0629
98 3UP3 XCA 10.2881
99 4EES FMN 10.4348
100 1XON PIL 10.8614
101 5BYK A3P 11.9691
102 5BYK OAQ 11.9691
103 4G86 BNT 11.985
104 1Q7E MET 13.1086
105 3PGL RZX 13.3333
106 4RJD TFP 13.6364
107 5C1M OLC 13.8514
108 5G5W R8C 14.2322
109 1NHZ 486 14.2322
110 4LSJ LSJ 14.7287
111 1M2Z DEX 14.786
112 4P6X HCY 14.902
113 3BQD DAY 14.902
114 4P6W MOF 15.0794
115 5Z84 CHD 15.2941
116 5W97 CHD 15.2941
117 5ZCO CHD 15.2941
118 4E2J MOF 15.6
119 3GN8 DEX 15.6627
120 5UFS 1TA 15.7258
121 2AX9 BHM 16.7969
122 3S0E EOL 16.8067
123 5UC1 486 17.1171
124 2Y69 CHD 18.5567
125 1ZEI CRS 18.8679
126 5ET3 60C 20
127 4OAR 2S0 20.5993
128 1SR7 MOF 20.5993
129 5MWY YNU 21.7228
130 5L7G 6QE 22.0974
131 4UDB CV7 22.0974
132 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 22.0974
133 3V49 PK0 22.1805
134 5HCV 60R 22.5681
135 2A3I C0R 22.9249
136 3RY9 1CA 26.9663
137 2Q1H AS4 30
138 1T0S BML 30.2326
139 1YYE 196 35.206
140 2I0G I0G 36.5759
141 2P54 735 36.7041
142 5WGQ EST 37.5479
143 5WGD EST 37.5479
144 5HYR EST 37.9845
145 1M13 HYF 38.2022
146 3G9E RO7 38.2022
147 5TWO 7MV 38.2022
148 2PRG BRL 38.2022
149 5DX3 EST 38.3142
150 5DXG EST 38.3142
151 5DXE EST 38.3142
152 1U3R 338 39.0042
153 4J24 EST 39.1667
154 3OLL EST 39.1667
155 4J26 EST 39.1667
156 2YJD YJD 39.1667
157 4MGD 27N 39.2157
158 4MG7 27H 39.2157
159 4MGB XDH 39.2157
160 4MG8 27J 39.2157
161 4MG9 27K 39.2157
162 4TUZ 36J 39.2157
163 4MGA 27L 39.2157
164 3UUD EST 39.8406
165 3UU7 2OH 39.8406
166 4TV1 36M 39.8406
167 3UUA 0CZ 39.8406
168 3BEJ MUF 39.916
169 3DCT 064 40.4255
170 2O4J VD4 40.4494
171 3OKI OKI 40.7725
172 2R40 20E 41.1985
173 2R40 EPH 41.1985
174 3RUU 37G 41.4847
175 5ICK FEZ 41.4847
176 5LGA 6VH 42.3221
177 5E7V M7E 42.3221
178 4Q0A 4OA 42.3221
179 3IPQ 965 42.6966
180 3H0A 9RA 44.7368
181 4OIV XX9 45.1327
182 6A5Y 9R0 45.1754
183 6A5Y 9CR 45.1754
184 6ESN BWE 45.3184
185 4DK7 0KS 45.3441
186 1N46 PFA 45.3488
187 3KFC 61X 45.8498
188 3L0E G58 46.2451
189 5NTW 98N 47.4708
190 5IXK 6EW 48.2456
191 3VRV YSD 49.0637
192 5XPL 8C9 49.0637
193 5NTP 98E 49.5798
194 3KDU NKS 49.8127
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