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 257 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 222 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 (131)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 3ILZ - B72 C20 H24 O4 Cc1cc(cc(c....
2 3HZF - B72 C20 H24 O4 Cc1cc(cc(c....
3 1NAV - IH5 C17 H16 Cl2 O4 CC(C)c1cc(....
4 4LNX - T44 C15 H11 I4 N O4 c1c(cc(c(c....
5 2H77 - T3 C15 H12 I3 N O4 c1cc(c(cc1....
6 2Q61 - SF1 C22 H16 Cl N O2 S c1ccc(cc1)....
7 3AN3 - M7S C37 H43 N O4 CCCOc1ccc(....
8 1ZEO ic50 = 0.21 uM C01 C25 H30 N O5 CCCc1cc2c(....
9 3R8I Kd = 4.5 uM XCX C26 H34 N2 O4 CCCCCCCN(C....
10 3ADW Kd = 72.8 uM MYI C11 H11 N O3 COc1ccc2c(....
11 4E4K - RRG C24 H24 O3 CC(C)c1ccc....
12 4XUH ic50 = 1.87 uM SFI C20 H17 F O2 S CC1=C(c2cc....
13 2POB - GW4 C36 H35 N3 O4 Cc1c(nc(o1....
14 2HWR - DRD C35 H35 N O5 CCCc1c2ccc....
15 4R2U - 3JX C33 H29 N3 O5 Cc1c(n(c2c....
16 2ZNO - S44 C32 H41 N O4 CCCOc1ccc(....
17 4XUM ic50 = 21.3 uM IMN C19 H16 Cl N O4 Cc1c(c2cc(....
18 3R5N Kd = 1.67 uM MLO C18 H18 O2 C=CCc1ccc(....
19 2HWQ - DRY C33 H31 N O5 CCCc1c2ccc....
20 3VJH - J35 C22 H24 F3 N O4 CCC[C@@H](....
21 3U9Q Ki = 41.7 uM DKA C10 H20 O2 CCCCCCCCCC....
22 2Q6R - SF2 C23 H18 Cl N O3 S COc1cccc(c....
23 2P4Y Ki = 0.001 uM C03 C28 H22 Cl F3 N2 O6 Cc1c(c2ccc....
24 3D6D - LRG C21 H18 O3 c1ccc(cc1)....
25 2F4B ic50 = 50 nM EHA C33 H31 N O5 CCCc1c2ccc....
26 3BC5 ic50 = 0.005 uM ZAA C29 H26 N4 O4 Cc1c(nc(o1....
27 3VSO - EK1 C31 H31 N3 O4 CCCOc1ccc(....
28 4R06 Kd = 565 nM 3E7 C28 H24 N2 O3 S CC[C@@H](c....
29 1I7I - AZ2 C20 H24 O7 S CCO[C@@H](....
30 4R6S - 3K2 C33 H29 N3 O5 Cc1c(n(c2c....
31 3GBK - 2PQ C38 H41 N O5 CCCc1cc(cc....
32 3SZ1 - LU2 C15 H10 O6 c1cc(c(cc1....
33 2ZVT - PTG C20 H28 O3 CCCCCC=CC=....
34 2ATH ic50 = 0.152 uM 3EA C24 H23 F3 N2 O5 CCCc1c(ccc....
35 4XLD - BRL C18 H19 N3 O3 S CN(CCOc1cc....
36 2G0H ic50 = 22.7 nM SP3 C21 H12 F7 N3 O2 S2 c1cc(sc1)c....
37 2Q5P - 241 C28 H24 F3 N O6 Cc1c(c2cc(....
38 2GTK ic50 = 0.251 uM 208 C24 H23 Cl N2 O4 CCO[C@@H](....
39 4Y29 ic50 = 566 nM CTI C21 H18 N O4 C[n+]1cc2c....
40 2I4J - DRJ C27 H36 N2 O4 CCCCCCCN(C....
41 3R8A - HIG C26 H25 N7 CCc1nc2c(c....
42 4XTA ic50 = 3.7 uM DIF C14 H11 Cl2 N O2 c1ccc(c(c1....
43 3TY0 ic50 = 83.1 nM 082 C26 H20 N4 O6 C[C@]1(C(=....
44 4YT1 - JJB C29 H28 N4 O5 S CCCOc1ccc(....
45 2ZK6 - C08 C22 H31 B F2 N2 O2 [B-]1(n2c(....
46 3ADS Kd = 9.73 uM IMN C19 H16 Cl N O4 Cc1c(c2cc(....
47 3ET0 - GLC C6 H12 O6 C([C@@H]1[....
48 4E4Q - RRH C24 H24 O3 CC(C)c1ccc....
49 1KNU - YPA C25 H25 N O4 CCO[C@@H](....
50 2Q8S ic50 = 0.185 uM L92 C26 H26 N2 O3 Cc1c(nc(o1....
51 2YFE Ki = 0.236 uM YFE C21 H24 O4 CC(=CCc1c(....
52 4EM9 - KNA C9 H18 O2 CCCCCCCCC(....
53 2Q6S - PLB C18 H11 Cl2 N3 O4 c1cnc(nc1)....
54 3AN4 - M7R C37 H43 N O4 CCCOc1ccc(....
55 3PBA - ZXG C15 H12 Br4 O5 S CC(C)(c1cc....
56 3ADV Kd = 933 uM SRO C10 H12 N2 O c1cc2c(cc1....
57 2Q5S - NZA C22 H15 Cl2 N O2 S c1ccc(cc1)....
58 5F9B - 5VN C30 H48 O5 C[C@]12CC[....
59 2I4P - DRH C27 H36 N2 O4 CCCCCCC[N@....
60 5LSG Kd = 4 uM QZQ C30 H46 O3 CC(=C)[C@@....
61 5TTO - 7KK C21 H11 Br Cl2 F2 N2 O3 S c1ccc2c(c1....
62 5HZC - 65W C20 H18 O3 CC(C)(C(=O....
63 3IA6 ic50 = 0.003 uM UNT C24 H24 N4 O3 Cc1c(nc(o1....
64 3ADX - IMN C19 H16 Cl N O4 Cc1c(c2cc(....
65 3HOD - ZZH C22 H20 O3 c1ccc(cc1)....
66 2I4Z - DRH C27 H36 N2 O4 CCCCCCC[N@....
67 2AWH - VCA C18 H34 O2 CCCCCCC=CC....
68 5U3Y - 7U7 C27 H29 N O5 c1ccc(c(c1....
69 5U3T - 7UY C27 H31 N O4 S CC(C)N(Cc1....
70 5U3X - 7U4 C28 H30 N2 O4 c1ccc(c(c1....
71 2BAW - VCA C18 H34 O2 CCCCCCC=CC....
72 5U3Z - 7UA C27 H29 N O5 c1ccc(c(c1....
73 5U3Q - 7UJ C29 H33 N O4 CC(C)N(Cc1....
74 5U45 - 7SY C29 H30 F N O4 c1ccc(c(c1....
75 3SP9 - IL2 C22 H32 O4 CC#CC[C@@H....
76 3GWX ic50 = 4 uM EPA C20 H30 O2 CCC=C/CC=C....
77 5U3V - 7TY C29 H33 N O5 c1ccc(c(c1....
78 2XYJ - WLM C21 H23 Cl N4 O4 S2 CC(C)c1nnc....
79 5U3S - 7V4 C27 H31 N O5 CC(C)N(Cc1....
80 5U3W - 7U1 C29 H31 N O4 c1ccc(cc1)....
81 5U40 - 7UD C31 H31 N O5 c1ccc(cc1)....
82 1GWX - 433 C28 H28 Cl3 F N2 O4 CC(C)(C(=O....
83 5U44 - 7SV C29 H30 F N O4 c1ccc(c(c1....
84 3TKM Kd = 22 nM GW0 C21 H17 F4 N O3 S2 Cc1cc(ccc1....
85 5U41 - 7UG C31 H31 N O4 S c1ccc(cc1)....
86 5U42 - 7SM C30 H33 N O5 COc1cccc(c....
87 5U3U - 7TV C29 H33 N O5 c1ccc(c(c1....
88 3GZ9 Ki = 0.004 uM D32 C27 H23 F3 O5 S Cc1c(c(ccc....
89 5U46 - 7T1 C21 H18 F3 N O3 S2 Cc1cc(ccc1....
90 5U3R - 7V1 C27 H31 N O5 CC(C)N(Cc1....
91 3ET2 - ET1 C19 H19 N O6 S COc1ccc(cc....
92 5U43 - 7SS C30 H33 N O5 COc1ccc(cc....
93 2B50 - VCA C18 H34 O2 CCCCCCC=CC....
94 3PEQ ic50 = 32 nM 3EQ C30 H31 N O5 S2 CCCC[N@@](....
95 4BCR - WY1 C14 H14 Cl N3 O2 S Cc1cccc(c1....
96 1I7G ic50 = 1 uM AZ2 C20 H24 O7 S CCO[C@@H](....
97 3KDU ic50 = 347 nM NKS C28 H25 Cl N2 O6 Cc1ccc(cc1....
98 3VI8 - 13M C30 H27 N O4 CC[C@@H](C....
99 2ZNN - S44 C32 H41 N O4 CCCOc1ccc(....
100 5HYK - 65W C20 H18 O3 CC(C)(C(=O....
101 1FD0 Kd ~ 4 nM 254 C26 H27 N O3 CC1(CCC(c2....
102 1FCX Kd = 64 nM 184 C26 H28 O3 CC1(CCC(c2....
103 1EXA - 394 C23 H26 F N O4 CC1(CCC(c2....
104 1EXX - 961 C23 H26 F N O4 CC1(CCC(c2....
105 5M24 - 9CR C20 H28 O2 CC1=C(C(CC....
106 1FCY Kd = 3 nM 564 C26 H26 O3 CC1(CCC(c2....
107 1N46 Ki = 0.03 nM PFA C20 H21 N3 O4 Cc1cc(cc(c....
108 2PIN - LEG C15 H20 O CCCCCCc1cc....
109 3GWS - T3 C15 H12 I3 N O4 c1cc(c(cc1....
110 2J4A - OEF C18 H18 Br2 O4 CC(C)c1cc(....
111 3D57 - 4HY C14 H9 I3 O4 c1cc(c(cc1....
112 1XZX Kd = 0.06 nM T3 C15 H12 I3 N O4 c1cc(c(cc1....
113 3JZC ic50 ~ 1 nM 4HY C14 H9 I3 O4 c1cc(c(cc1....
114 1NQ0 - 4HY C14 H9 I3 O4 c1cc(c(cc1....
115 3CS4 - COV C28 H44 O4 C[C@]12CCC....
116 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
117 3M7R - VDX C27 H44 O3 C[C@H](CCC....
118 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
119 3TKC - FMV C28 H40 O4 C[C@H](c1c....
120 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
121 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
122 1M13 Kd = 27 nM HYF C35 H52 O4 CC(C)C(=O)....
123 4X1F Ki = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
124 5K13 Ki = 1.8 nM 6Q7 C27 H26 N2 O4 S CC(C)(C)c1....
125 1UPV - 444 C17 H12 F9 N O3 S c1ccc(cc1)....
126 3KFC ic50 = 2.8 nM 61X C23 H16 F3 N O3 S CS(=O)(=O)....
127 1XAP Kd = 2.5 nM TTB C24 H28 O2 C/C(=Cc1cc....
128 2LBD - REA C20 H28 O2 CC1=C(C(CC....
129 4LBD - 961 C23 H26 F N O4 CC1(CCC(c2....
130 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
131 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
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: 93
This union binding pocket(no: 1) in the query (biounit: 1xap.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4UY1 TJM 0.01862 0.40052 1.52672
2 5CX8 TG6 0.01451 0.42444 2.24719
3 3IA4 MTX 0.0102 0.40532 2.46914
4 4XNV BUR 0.02029 0.41351 2.62172
5 2ZCQ B65 0.02107 0.40338 2.62172
6 4URN NOV 0.01513 0.41349 2.66667
7 2WTN FER 0.002783 0.44574 2.78884
8 3KYQ DPV 0.02612 0.40127 3.01508
9 5VRH OLB 0.02872 0.40246 3.06513
10 4CCW VKC 0.01462 0.40163 3.37079
11 3GUZ PAF 0.01587 0.41032 3.40909
12 1L0I PSR 0.02838 0.40678 3.84615
13 4E90 7RG 0.005555 0.4048 4.86891
14 2V0U FMN 0.004784 0.40918 5.47945
15 5DJT FMN 0.003269 0.40892 5.51724
16 5DJU FMN 0.005621 0.40277 5.51724
17 4UBS DIF 0.03187 0.40083 5.61798
18 2Q8H TF4 0.0292 0.40037 6.36704
19 1DTL BEP 0.007739 0.41488 7.45342
20 5DKK FMN 0.007091 0.40177 7.58621
21 4RW3 TDA 0.02927 0.41667 7.86517
22 1XZ3 ICF 0.01361 0.42773 8.04598
23 3G08 FEE 0.0224 0.40921 8.08081
24 5J32 IPM 0.01075 0.42329 8.2397
25 4UCC ZKW 0.04483 0.40356 8.58369
26 3NV6 CAM 0.005438 0.43023 8.61423
27 3GXO MQA 0.01901 0.4041 8.61423
28 4EES FMN 0.006297 0.40068 10.4348
29 4RJD TFP 0.009522 0.42374 13.6364
30 1NHZ 486 0.0002571 0.46367 14.2322
31 5G5W R8C 0.00008254 0.44091 14.2322
32 4LSJ LSJ 0.00002513 0.50458 14.7287
33 1M2Z DEX 0.00002208 0.50455 14.786
34 4P6X HCY 0.00005398 0.48813 14.902
35 3BQD DAY 0.0001089 0.47749 14.902
36 4P6W MOF 0.00008465 0.46471 15.0794
37 4E2J MOF 0.00003712 0.47925 15.6
38 3GN8 DEX 0.0001128 0.4746 15.6627
39 5UFS 1TA 0.00006468 0.46963 15.7258
40 2AX9 BHM 0.0004069 0.47926 16.7969
41 2Y69 CHD 0.02762 0.40885 18.5567
42 4OAR 2S0 0.000003089 0.54066 20.5993
43 1SR7 MOF 0.00002156 0.52543 20.5993
44 5L7G 6QE 0.00002146 0.50982 22.0974
45 4UDB CV7 0.00003974 0.46433 22.0974
46 3V49 PK0 0.0002907 0.46524 22.1805
47 5HCV 60R 0.0003527 0.45366 22.5681
48 2A3I C0R 0.00004779 0.4927 22.9249
49 3RY9 1CA 0.0001852 0.47513 26.9663
50 2Q1H AS4 0.0003165 0.45128 30
51 1YYE 196 0.00001327 0.49121 35.206
52 2I0G I0G 0.0001465 0.50965 36.5759
53 5HYR EST 0.000005718 0.55553 37.9845
54 3FUR Z12 0.00197 0.45303 38.2022
55 3G9E RO7 0.00223 0.43848 38.2022
56 5TWO 7MV 0.002416 0.41831 38.2022
57 5DX3 EST 0.00000329 0.57433 38.3142
58 5DXG EST 0.000005089 0.56537 38.3142
59 5DXE EST 0.000007824 0.54924 38.3142
60 1U3R 338 0.00002783 0.51146 39.0042
61 4J26 EST 0.000003428 0.57348 39.1667
62 3OLL EST 0.000005374 0.50929 39.1667
63 4J24 EST 0.00000409 0.50163 39.1667
64 2YJD YJD 0.00008704 0.49512 39.1667
65 4MGA 27L 0.00002328 0.5555 39.2157
66 4MGD 27N 0.000007669 0.54964 39.2157
67 4MG7 27H 0.000001115 0.54486 39.2157
68 4MGB XDH 0.000001318 0.54218 39.2157
69 4MG8 27J 0.00001342 0.53842 39.2157
70 4TUZ 36J 0.00007631 0.50978 39.2157
71 4MG9 27K 0.000003161 0.48009 39.2157
72 3UU7 2OH 0.00004012 0.54512 39.8406
73 4TV1 36M 0.00007855 0.53024 39.8406
74 3UUD EST 0.000003392 0.51141 39.8406
75 3UUA 0CZ 0.0001163 0.5075 39.8406
76 3BEJ MUF 0.00007034 0.48776 39.916
77 3DCT 064 0.00004676 0.49956 40.4255
78 2O4J VD4 0.00007218 0.44401 40.4494
79 2R40 20E 0.0001676 0.44212 41.1985
80 5ICK FEZ 0.0001036 0.4811 41.4847
81 3RUU 37G 0.000009914 0.46405 41.4847
82 5E7V M7E 0.00009342 0.49384 42.3221
83 4Q0A 4OA 0.004395 0.41077 42.3221
84 5LGA 6VH 0.00008574 0.40978 42.3221
85 3IPQ 965 0.0000001061 0.51748 42.6966
86 3H0A 9RA 0.00006713 0.47882 44.7368
87 1XIU REA 0.00004704 0.5014 44.7826
88 4DK7 0KS 0.00001138 0.52251 45.3441
89 3JZB 4HY 0.00003677 0.45098 45.6929
90 3L0E G58 0.0000003106 0.59856 46.2451
91 5IXK 6EW 0.003675 0.41059 48.2456
92 4ZOM 4Q3 0.002697 0.46423 48.8889
93 3VRV YSD 0.00009988 0.51534 49.0637
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