Receptor
PDB id Resolution Class Description Source Keywords
5mku 1.78 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF THE RETINOID X RECEPTOR ALPHA IN COMPLE SYNTHETIC HONOKIOL DERIVATIVE 4 AND A FRAGMENT OF THE TIF2 A CTIVATOR. HOMO SAPIENS RXR TIF2 HONOKIOL TRANSCRIPTION
Ref.: LIGAND DEPENDENT SWITCH FROM RXR HOMO- TO RXR-NURR1 HETERODIMERIZATION. ACS CHEM NEUROSCI V. 8 2065 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
J57 A:501;
 Valid;
 none;
 submit data
282.334 C18 H18 O3 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4M8E 2.4 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF HUMAN RETINOID X RECEPTOR ALPHA-LIGAND DOMAIN COMPLEX WITH (S) 4-METHYL 9CUAB30 COACTIVATOR PEPTID HOMO SAPIENS ANTIPARALLEL SANDWICH LIGAND BINDING COACTIVATOR BINDING DIMERIZATION ACTIVATION FUNCTION TRANSCRIPTION NUCLEAR RLIGAND BINDING DOMIAN LIGAND BINDING POCKET COACTIVATOR BSITE CANCER 4-METHYL 9CUAB30 ((2E 4E 6Z 8E)-8-[(4-prime S)ME4-prime -DIHYDRO-1-prime (2-prime H)-NAPHTHALEN-1-prime -YLIDENE]-3 7-DIMETHYL-2 OCTATRIENOIC ACID)
Ref.: METHYL-SUBSTITUTED CONFORMATIONALLY CONSTRAINED REX AGONISTS FOR THE RETINOID X RECEPTORS DEMONSTRATE I EFFICACY FOR CANCER THERAPY AND PREVENTION. BIOORG.MED.CHEM. V. 22 178 2014
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 308 families.
1 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
2 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
3 5MK4 - I5W C22 H18 O3 Cc1ccc(cc1....
4 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
5 3OAP Kd = 14 nM 9CR C20 H28 O2 CC1=C(C(CC....
6 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
7 5MKU - J57 C18 H18 O3 CC(C)c1ccc....
70% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 2P1T - 3TN C24 H28 O4 CC1(CCC(c2....
2 4OC7 - 2QO C18 H16 O3 C=CCc1cccc....
3 5MJ5 - 7O0 C22 H18 O3 c1ccc(cc1)....
4 4RMD Kd = 35 nM 3SW C24 H34 O2 CC(C)CCC1=....
5 4K4J - 1O8 C20 H22 O2 C/C(=CC(=O....
6 4PP5 Kd = 18 nM 2W0 C21 H24 O2 Cc1cccc2c1....
7 4PP3 Kd = 15 nM 2VZ C21 H24 O2 Cc1ccc2c(c....
8 4POH Kd = 10 nM 2VR C21 H24 O2 Cc1cccc2c1....
9 2P1U - 4TN C25 H30 O4 CCOc1cc2c(....
10 1MV9 - HXA C22 H32 O2 CCC=C/CC=C....
11 4RFW Kd = 9 nM 3RB C21 H24 O2 C/C(=CC(=O....
12 3FUG - 2E3 C24 H28 O3 Cc1cc2c(cc....
13 6STI - 754 C26 H36 O3 CCCOc1cc2c....
14 3E94 - TBY C12 H27 Sn CCCC[Sn](C....
15 4POJ Kd = 8 nM 2VP C21 H24 O2 Cc1ccc2c(c....
16 4K6I - 9RA C24 H28 O2 Cc1cc2c(cc....
17 2P1V - 5TN C26 H32 O4 CCCOc1cc2c....
18 7A77 - PLM C16 H32 O2 CCCCCCCCCC....
19 4ZSH Kd = 90 nM 4XW C20 H36 O2 C[C@H]1CC=....
20 3KWY - T9T C18 H15 Sn c1ccc(cc1)....
21 4RME Kd = 9 nM 3T2 C24 H36 O2 CC(C)CCC1=....
22 1MZN - BM6 C24 H27 O4 CC1(CCC(c2....
23 1MVC - BM6 C24 H27 O4 CC1(CCC(c2....
24 5LYQ - 7BE C26 H30 O4 CC1(CCC(c2....
25 7A78 - PLM C16 H32 O2 CCCCCCCCCC....
26 1XIU - 9CR C20 H28 O2 CC1=C(C(CC....
27 7A79 - PLM C16 H32 O2 CCCCCCCCCC....
28 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
29 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
30 5MK4 - I5W C22 H18 O3 Cc1ccc(cc1....
31 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
32 3OAP Kd = 14 nM 9CR C20 H28 O2 CC1=C(C(CC....
33 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
34 5MKU - J57 C18 H18 O3 CC(C)c1ccc....
50% Homology Family (149)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 families.
1 5EHJ - 5K5 C23 H26 O2 c1cc(ccc1C....
2 4ZN7 - DES C18 H20 O2 CC/C(=C(/C....
3 5KCT ic50 = 0.43 uM OB7 C26 H24 Cl N O5 S CCN(c1ccc(....
4 5TN6 - 7G1 C18 H24 O2 C[C@]12CC[....
5 5TLD - 6WV C24 H29 N O C[C@]12CC[....
6 5KRA - 6WS C14 H8 Cl4 c1cc(ccc1C....
7 5DIG - 5CE C17 H21 F3 O2 C[C@]12CC[....
8 2FAI Ki = 570 nM 459 C17 H24 O3 CC1CC[C@@]....
9 5TLL - 7EL C13 H10 Cl N O3 c1cc(ccc1c....
10 4ZNS - OFB C24 H19 F O6 S c1cc(cc(c1....
11 2B1Z ic50 = 79 nM 17M C19 H22 O2 C[C@]12CCc....
12 5DRM - 5ET C16 H10 Cl2 O2 S c1cc(c(cc1....
13 5DI7 - 5CQ C17 H24 O2 Cc1cc(ccc1....
14 5DU5 - 5G2 C16 H10 Cl2 O4 S c1cc(c(cc1....
15 5TM4 - 7E3 C29 H27 Cl O8 S c1cc(cc(c1....
16 5TMS - 7FG C27 H30 O3 CCOC(=O)C=....
17 7JHD - V9J C20 H13 F O3 S c1cc(ccc1c....
18 5DXR - 5HW C20 H22 O2 C[C@@H]1CC....
19 2P15 - EZT C27 H29 F3 O2 C[C@]12CC[....
20 4ZNU - 4Q9 C25 H22 O6 S Cc1ccccc1O....
21 5TMZ - 7FQ C26 H32 O3 C[C@]12CC[....
22 5KRL - 6WR C15 H17 Cl O2 c1cc(c(cc1....
23 1X7R ic50 = 360 nM GEN C15 H10 O5 c1cc(ccc1C....
24 5TN7 - 7G2 C13 H10 F N O3 c1cc(c(cc1....
25 5TMO - 7M1 C24 H18 O5 S c1ccc(cc1)....
26 2QR9 - HZ3 C22 H18 O7 COC(=O)C1=....
27 5KRH - 6WN C25 H26 O2 C[C@]12CC[....
28 5DZH - 5KG C21 H24 O3 c1cc(ccc1C....
29 5KCD ic50 = 0.74 uM OB2 C25 H23 N O5 S CN(c1ccccc....
30 5TMM - 7M4 C30 H27 Br O7 S c1cc(ccc1C....
31 5E0W - 5KE C25 H24 O3 c1cc(ccc1[....
32 5TLO - 7EE C26 H29 N O2 C[C@]12CC[....
33 5TLX - 7EH C13 H12 N4 Cn1c2c(cc(....
34 5KRO - 6WW C25 H31 N O C[C@]12CC[....
35 5E19 - 5K7 C22 H24 O4 COC(=O)CC1....
36 5KCE ic50 = 0.45 uM OB3 C25 H22 Cl N O5 S CN(c1ccccc....
37 5DL4 - 5C4 C27 H23 N O2 CC(=C(c1cc....
38 5DVS - 5G7 C20 H17 N O2 Cc1ccccc1N....
39 5DID - 5CK C16 H20 F2 O2 C[C@]12CC[....
40 5KRI - 6WM C25 H30 O2 C[C@]12CC[....
41 5KCW ic50 = 0.19 uM OB9 C26 H22 F3 N O5 S c1ccc(cc1)....
42 5TM8 - 7K6 C31 H31 Br O8 S c1cc(ccc1C....
43 4ZN9 - OBH C24 H22 O6 S c1cc(ccc1C....
44 5KRC - ZER C18 H22 O5 C[C@H]1CCC....
45 1ZKY Ki = 560 nM 689 C18 H24 O3 C[C@H]1C=C....
46 5DXP - 5HX C22 H24 O c1ccc(cc1)....
47 5DMF - 5DG C27 H22 F N O2 CC(=C(c1cc....
48 5TMU - 7FL C20 H22 O2 c1cc(ccc1C....
49 5AAV ic50 = 3.24 nM GW5 C25 H22 O2 CC/C(=C(c1....
50 2B1V Ki = 1.8 uM 458 C16 H20 O3 CC1=CC[C@]....
51 5DUG - 5FV C26 H24 O6 S2 Cc1cc(ccc1....
52 5E0X - 5KD C26 H26 O3 COc1ccc(cc....
53 5KCC - OB1 C24 H21 N O5 S c1ccc(cc1)....
54 4MG5 - 27E C10 Cl10 O C1(=O)C2([....
55 5KCU ic50 = 6.49 uM OB8 C30 H27 N O5 S CCN(c1ccc2....
56 5DLR - 5DJ C20 H16 O2 c1ccc(cc1)....
57 3ERD - DES C18 H20 O2 CC/C(=C(/C....
58 2YJA - EST C18 H24 O2 C[C@]12CC[....
59 5TLU - 7EE C26 H29 N O2 C[C@]12CC[....
60 5DMC - 5DH C21 H15 N O2 c1ccc(cc1)....
61 4ZNT - OBB C24 H19 Br O6 S c1cc(cc(c1....
62 5DXM - 5J0 C22 H24 O2 c1cc(cc(c1....
63 5DK9 - 5CC C28 H25 N O2 CCC(=C(c1c....
64 5TLG - 7EG C19 H15 N O4 c1cc(ccc1c....
65 4MGC - 27M C13 H10 O5 c1cc(c(cc1....
66 5TLP - 7ET C31 H32 F N O6 S c1cc(cc(c1....
67 5U2D - OBH C24 H22 O6 S c1cc(ccc1C....
68 4MG6 - 27G C19 H20 O4 CCCCOC(=O)....
69 2JF9 - OHT C26 H29 N O2 CC/C(=C(c1....
70 5TLV - 7ES C16 H10 F2 O2 S c1cc(c(cc1....
71 5KRM - 6WU C16 H18 F2 O2 C[C@]12CC=....
72 5DUH - 5FT C26 H24 O6 S2 Cc1cc(ccc1....
73 4ZNV - 4Q7 C25 H22 O7 S COc1ccccc1....
74 2QGW - EES C13 H9 Cl N2 O2 c1cc(ccc1n....
75 5KR9 - CUE C15 H8 O5 c1cc2c(cc1....
76 5DTV - 5FS C18 H16 O4 S Cc1cc(ccc1....
77 5DY8 - 5K4 C21 H24 O2 CC[C@H]1CC....
78 5KRK - 6WQ C22 H17 Br O2 c1cc(ccc1C....
79 4PPS - ESE C16 H22 O2 C[C@]12CC[....
80 1L2I - ETC C22 H24 O2 CC[C@@H]1C....
81 5DWG - 5G4 C20 H17 N O3 Cc1ccccc1/....
82 5KD9 ic50 = 0.93 uM OBT C26 H21 Cl F3 N O5 S c1cc(ccc1C....
83 4ZNH - OBC C24 H19 F O6 S c1ccc(c(c1....
84 5DKB - 5C9 C29 H27 N O2 CCC(=C(c1c....
85 5KRF - 6WL C15 H11 F3 N2 O2 Cn1c2c(ccc....
86 2QGT - EED C20 H28 O3 C[C@]12C[C....
87 2QAB - EI1 C15 H14 N2 O2 CCc1c2cc(c....
88 5DYB - 5K2 C23 H20 O2 c1ccc2c(c1....
89 5E15 - 5KA C25 H31 F O3 c1cc(ccc1C....
90 5DKG - 5C7 C25 H26 O2 CC(=C(c1cc....
91 5DUE - 5FY C26 H24 O7 S2 Cc1cc(ccc1....
92 3OS8 - KN0 C21 H15 F3 N2 O2 c1ccc(cc1)....
93 5KCF ic50 = 0.72 uM OB4 C27 H27 N O6 S CCN(c1ccc(....
94 5DXK - 5J1 C22 H26 O2 c1cc(ccc1C....
95 5TLM - 7EM C22 H16 O3 S c1cc(ccc1c....
96 5E14 - 5KB C25 H24 O2 c1ccc(cc1)....
97 5DWJ - 5J2 C19 H14 F N O3 c1cc(ccc1/....
98 5DRJ - 5EU C17 H12 Cl2 O2 S Cc1cc(sc1c....
99 5TM9 - 7KL C27 H21 Cl O7 S c1cc(cc(c1....
100 5TMV - 7FO C24 H19 I O6 S c1cc(ccc1C....
101 5TM5 - 7EV C29 H27 Br O8 S c1cc(ccc1C....
102 5TMT - 7FJ C22 H18 O2 c1ccc2c(c1....
103 5DXQ - 5HZ C22 H24 O2 c1cc(ccc1C....
104 2QXM - PIQ C13 H12 N4 Cn1c2cc(cn....
105 5E1C - 5K8 C24 H26 O6 COC(=O)C([....
106 5TM3 - 7EN C16 H10 Cl2 O3 S c1cc(c(cc1....
107 5TM7 - 7JY C31 H31 Cl O8 S c1cc(cc(c1....
108 5TMR - 7FD C24 H26 O3 CCOC(=O)C=....
109 5DZ0 - 5K0 C20 H22 O2 CC1CCC(=C(....
110 5DP0 - 5ES C26 H20 F N O2 c1cc(cc(c1....
111 5TLT - 7ED C42 H50 O8 CC[C@H](c1....
112 4PXM - EST C18 H24 O2 C[C@]12CC[....
113 5TN4 - 7FZ C17 H18 O2 Cc1cc(cc(c....
114 5TMW - 7FP C26 H23 N O7 S CC(=O)Nc1c....
115 5DYD - 5K1 C20 H22 O2 S CS[C@H]1CC....
116 5TLF - 7EF C19 H17 F3 N2 O2 CC(=CCn1c(....
117 5DZ3 - 5JX C20 H21 F O2 c1cc(ccc1C....
118 5TN1 - 7FR C27 H33 N O CC(C)c1ccc....
119 5DWI - 5G3 C19 H14 Cl N O3 c1ccc(c(c1....
120 5TN5 - 7G0 C16 H22 O2 C[C@]12CC[....
121 2QSE - 1HP C13 H12 N4 O Cn1c2cc(cn....
122 5TML - 7E1 C30 H27 Cl O7 S c1cc(cc(c1....
123 5DZI - 5KF C21 H24 O3 c1cc(ccc1C....
124 5DWE - 5G5 C19 H14 Cl N O2 c1ccc(c(c1....
125 4DMA - 0L8 C17 H13 Br O3 c1cc(ccc1c....
126 5TLY - 7ER C16 H10 F2 O4 S c1cc(c(cc1....
127 4ZNW - OBM C24 H19 Br O6 S c1cc(ccc1C....
128 5TMQ - 7M7 C24 H17 Br O5 S c1cc(ccc1c....
129 5EI1 - 5OR C13 H9 I N2 O2 c1cc(ccc1c....
130 5DZ1 - 5JY C21 H24 O2 CCC1CCC(=C....
131 5DIE - 5CJ C16 H19 F3 O2 C[C@]12CC[....
132 6CBZ - EST C18 H24 O2 C[C@]12CC[....
133 1MZN - BM6 C24 H27 O4 CC1(CCC(c2....
134 1MVC - BM6 C24 H27 O4 CC1(CCC(c2....
135 5LYQ - 7BE C26 H30 O4 CC1(CCC(c2....
136 3OMQ - W23 C10 H10 F3 N O3 S c1cc2c(cc1....
137 3OMO - WV7 C11 H10 F3 N O2 c1cc2c(cc1....
138 3OLL - EST C18 H24 O2 C[C@]12CC[....
139 3OLS - EST C18 H24 O2 C[C@]12CC[....
140 6LIT - 2OH C15 H16 O2 CC(C)(c1cc....
141 1X78 ic50 = 14 nM 244 C16 H11 N O3 c1cc(ccc1c....
142 1U3S ic50 = 1.4 nM 797 C17 H11 N O3 c1cc(cc2c1....
143 1U3R ic50 = 5 nM 338 C17 H11 N O3 c1cc2c(ccc....
144 1X7B ic50 = 4.1 nM 041 C15 H10 F N O3 C=Cc1cc(cc....
145 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
146 5MKU - J57 C18 H18 O3 CC(C)c1ccc....
147 4J26 - EST C18 H24 O2 C[C@]12CC[....
148 1YYE ic50 = 2.7 nM 196 C17 H10 F N O2 c1cc(cc2c1....
149 4J24 - EST C18 H24 O2 C[C@]12CC[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: J57; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 J57 1 1
2 2QO 0.557143 0.785714
3 7O0 0.541667 0.814815
4 I5W 0.447368 0.884615
5 DHC 0.416667 0.678571
6 3TN 0.405063 0.735294
7 FER 0.4 0.689655
Similar Ligands (3D)
Ligand no: 1; Ligand: J57; Similar ligands found: 20
No: Ligand Similarity coefficient
1 M8Q 0.9264
2 S2X 0.9163
3 KC6 0.9049
4 QIU 0.9019
5 7WH 0.8974
6 T7O 0.8967
7 43H 0.8896
8 E8B 0.8893
9 C9Q 0.8824
10 4ZK 0.8802
11 MLO 0.8795
12 61Y 0.8792
13 0RA 0.8779
14 EFX 0.8735
15 JI1 0.8668
16 AV7 0.8655
17 43G 0.8633
18 76Z 0.8620
19 6Z1 0.8620
20 2WF 0.8601
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4M8E; Ligand: 29V; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 4m8e.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1YYE 196 42.8571
2 1U3R 338 42.8571
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