Receptor
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 ((2E4E6Z8E)-8-[(4-prime S)METHYDIHYDRO-1-prime (2-prime H)-NAPHTHALEN-1-prime -YLIDENE]-37-DIMETHYL-246- 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
29V A:500;
Valid;
none;
Kd = 13 nM
310.43 C21 H26 O2 C[C@H...
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 ((2E4E6Z8E)-8-[(4-prime S)METHYDIHYDRO-1-prime (2-prime H)-NAPHTHALEN-1-prime -YLIDENE]-37-DIMETHYL-246- 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 (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 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 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
4 3OAP Kd = 14 nM REA C20 H28 O2 CC1=C(C(CC....
5 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
70% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 2P1T - 3TN C24 H28 O4 CC1(CCC(c2....
2 4OC7 - 2QO C18 H16 O3 C=CCc1cccc....
3 4RMD Kd = 35 nM 3SW C24 H34 O2 CC(C)CCC1=....
4 4K4J - 1O8 C20 H22 O2 C/C(=CC(=O....
5 4PP5 Kd = 18 nM 2W0 C21 H24 O2 Cc1cccc2c1....
6 4PP3 Kd = 15 nM 2VZ C21 H24 O2 Cc1ccc2c(c....
7 4POH Kd = 10 nM 2VR C21 H24 O2 Cc1cccc2c1....
8 2P1U - 4TN C25 H30 O4 CCOc1cc2c(....
9 1MV9 - HXA C22 H32 O2 CCC=C/CC=C....
10 4RFW Kd = 9 nM 3RB C21 H24 O2 C/C(=CC(=O....
11 3FUG - 2E3 C24 H28 O3 Cc1cc2c(cc....
12 3E94 - TBY C12 H27 Sn CCCC[Sn](C....
13 4POJ Kd = 8 nM 2VP C21 H24 O2 Cc1ccc2c(c....
14 4K6I - 9RA C24 H28 O2 Cc1cc2c(cc....
15 2P1V - 5TN C26 H32 O4 CCCOc1cc2c....
16 4ZSH Kd = 90 nM 4XW C20 H36 O2 C[C@H]1CC=....
17 3KWY - T9T C18 H15 Sn c1ccc(cc1)....
18 4RME Kd = 9 nM 3T2 C24 H36 O2 CC(C)CCC1=....
19 1MZN - BM6 C24 H27 O4 CC1(CCC(c2....
20 1MVC - BM6 C24 H27 O4 CC1(CCC(c2....
21 5LYQ - 7BE C26 H30 O4 CC1(CCC(c2....
22 1XIU - REA C20 H28 O2 CC1=C(C(CC....
23 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
24 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
25 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
26 3OAP Kd = 14 nM REA C20 H28 O2 CC1=C(C(CC....
27 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 2P1T - 3TN C24 H28 O4 CC1(CCC(c2....
2 4OC7 - 2QO C18 H16 O3 C=CCc1cccc....
3 4RMD Kd = 35 nM 3SW C24 H34 O2 CC(C)CCC1=....
4 4K4J - 1O8 C20 H22 O2 C/C(=CC(=O....
5 4PP5 Kd = 18 nM 2W0 C21 H24 O2 Cc1cccc2c1....
6 4PP3 Kd = 15 nM 2VZ C21 H24 O2 Cc1ccc2c(c....
7 4POH Kd = 10 nM 2VR C21 H24 O2 Cc1cccc2c1....
8 2P1U - 4TN C25 H30 O4 CCOc1cc2c(....
9 1MV9 - HXA C22 H32 O2 CCC=C/CC=C....
10 4RFW Kd = 9 nM 3RB C21 H24 O2 C/C(=CC(=O....
11 3FUG - 2E3 C24 H28 O3 Cc1cc2c(cc....
12 3E94 - TBY C12 H27 Sn CCCC[Sn](C....
13 4POJ Kd = 8 nM 2VP C21 H24 O2 Cc1ccc2c(c....
14 4K6I - 9RA C24 H28 O2 Cc1cc2c(cc....
15 2P1V - 5TN C26 H32 O4 CCCOc1cc2c....
16 4ZSH Kd = 90 nM 4XW C20 H36 O2 C[C@H]1CC=....
17 3KWY - T9T C18 H15 Sn c1ccc(cc1)....
18 4RME Kd = 9 nM 3T2 C24 H36 O2 CC(C)CCC1=....
19 1MZN - BM6 C24 H27 O4 CC1(CCC(c2....
20 1MVC - BM6 C24 H27 O4 CC1(CCC(c2....
21 5LYQ - 7BE C26 H30 O4 CC1(CCC(c2....
22 1XIU - REA C20 H28 O2 CC1=C(C(CC....
23 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
24 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
25 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
26 3OAP Kd = 14 nM REA C20 H28 O2 CC1=C(C(CC....
27 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 29V; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 29V 1 1
2 R4M 0.621622 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4M8E; Ligand: 29V; Similar sites found: 131
This union binding pocket(no: 1) in the query (biounit: 4m8e.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1QY8 RDI 0.004882 0.41974 None
2 4WGF HX2 0.01896 0.4178 None
3 1JX6 AI2 0.02586 0.40701 None
4 5CSD ACD 0.01191 0.40332 None
5 5BVT PAM 0.006853 0.40261 None
6 1RL4 BRR 0.01668 0.41461 1.59574
7 3OQJ 3CX 0.0194 0.4112 1.7316
8 4OR7 25U 0.01321 0.41116 1.81818
9 3LE7 ADE 0.02241 0.4097 2.1645
10 4DOO DAO 0.008841 0.40441 2.43902
11 1YC4 43P 0.002025 0.44622 2.5974
12 4MC3 28U 0.02422 0.40619 2.5974
13 3GUZ PAF 0.0188 0.4153 2.84091
14 1A05 IPM 0.003666 0.45073 3.0303
15 5J32 IPM 0.006877 0.43673 3.0303
16 3LXI CAM 0.02601 0.40663 3.0303
17 4V3I ASP LEU THR ARG PRO 0.008768 0.43672 3.4632
18 1VRP IOM 0.01806 0.41155 3.4632
19 5B4B LP5 0.005937 0.40939 3.4632
20 1CZA ADP 0.02613 0.40843 3.4632
21 1SBR VIB 0.004331 0.44493 3.5
22 1HFU NAG NDG 0.0206 0.41515 3.8961
23 2XEM SSV 0.005783 0.42879 4
24 4R29 SAM 0.02208 0.40408 4.01786
25 2OCI TYC 0.0265 0.40382 4.329
26 5CX8 TG6 0.0403 0.40137 4.329
27 3ZJQ NCA 0.008847 0.4181 4.61538
28 1TV5 N8E 0.0009704 0.49496 4.7619
29 4ORM 2V6 0.02206 0.41016 4.7619
30 4ORM ORO 0.02206 0.41016 4.7619
31 4ORM FMN 0.02206 0.41016 4.7619
32 1SQL GUN 0.02519 0.40509 4.79452
33 5UC9 MYR 0.008586 0.42481 4.86726
34 2BYC FMN 0.01427 0.40189 5.10949
35 2GBB CIT 0.01986 0.41067 5.12821
36 1YTM OXD 0.03109 0.40297 5.19481
37 3G4Q MCH 0.01323 0.40716 5.47945
38 3R9V DXC 0.01831 0.41629 5.62771
39 4O4Z N2O 0.02917 0.4053 5.84416
40 2VWA PTY 0.02419 0.41072 5.94059
41 5LX9 OLB 0.003748 0.42909 6.06061
42 4XCP PLM 0.02328 0.40412 6.06061
43 2Z49 AMG 0.0448 0.40287 6.06061
44 4NMC FAD 0.01381 0.40152 6.06061
45 4NMC 2OP 0.01309 0.40152 6.06061
46 2WDQ CBE 0.01777 0.4159 6.08696
47 4MRP GSH 0.005446 0.44838 6.49351
48 4RW3 TDA 0.01253 0.44822 6.49351
49 2JAP J01 0.01698 0.40986 6.49351
50 5CQG 55C 0.03456 0.40285 6.49351
51 4P3H 25G 0.001485 0.41094 6.73575
52 3NJQ NJQ 0.009002 0.40757 6.73575
53 5V4R MGT 0.01685 0.4221 6.79012
54 2CB8 MYA 0.01375 0.42279 6.89655
55 3HP9 CF1 0.009724 0.4338 6.92641
56 3KU0 ADE 0.02424 0.40999 6.92641
57 3G3N TC8 0.01567 0.41812 7.35931
58 4YSX E23 0.009344 0.42766 7.69231
59 3GL0 HXX 0.002055 0.44592 7.79221
60 3RET PYR 0.009472 0.41024 7.92079
61 3RET SAL 0.009472 0.41024 7.92079
62 4URN NOV 0.02797 0.40291 8.44444
63 4MUV PCG 0.006634 0.41749 8.4507
64 3CHT 4NB 0.01857 0.4098 8.65801
65 5OCA 9QZ 0.01063 0.43394 8.73016
66 3TL1 JRO 0.01423 0.41819 8.80503
67 3RV5 DXC 0.00008761 0.41553 8.98876
68 5LWY OLB 0.002475 0.43751 9.34579
69 1BRW URA 0.02547 0.40593 9.52381
70 1DLL LAT 0.027 0.40469 9.95671
71 1Y75 NAG 0.02426 0.402 10.1695
72 3PMA SCR 0.01065 0.42331 10.8225
73 5KOD IAC 0.003162 0.44208 11.2554
74 1HN4 MJI 0.0165 0.41669 11.4504
75 2JHP GUN 0.01229 0.41886 12.1212
76 5UGW GSH 0.002452 0.42736 13.1429
77 2QJY UQ2 0.01134 0.42331 13.4199
78 3N7S 3N7 0.007952 0.43847 14.5833
79 3B6R CRN 0.007993 0.42257 16.0173
80 1ZEI CRS 0.009295 0.42778 16.9811
81 3WBG 2AN 0.002116 0.43633 16.9935
82 5CKS GAL 0.01096 0.4192 17.7489
83 5HZ9 5M8 0.004254 0.41498 19.2593
84 2XN5 FUN 0.01079 0.41549 20
85 2Y69 CHD 0.00479 0.4503 22.8571
86 5APK 76E 0.000009877 0.52398 23.3766
87 5NTW 98N 0.00007836 0.48946 23.3766
88 5IXK 6EW 0.0003662 0.4571 23.6842
89 4ZOM 4Q3 0.0001712 0.43698 24
90 1NHZ 486 0.000004669 0.53816 24.2424
91 5G5W R8C 0.000001216 0.51582 24.2424
92 3BQD DAY 0.0000003687 0.56484 27.2727
93 1M2Z DEX 0.000001719 0.55672 27.2727
94 4P6W MOF 0.000001577 0.54604 27.2727
95 1M2Z BOG 0.003647 0.47628 27.2727
96 4LSJ LSJ 0.00156 0.45144 27.2727
97 4P6X HCY 0.000001778 0.53104 28.1385
98 3RY9 1CA 0.00000004929 0.63895 29.4372
99 4E2J MOF 0.00000056 0.56452 29.4372
100 5UFS 1TA 0.00000064 0.56214 29.4372
101 3GN8 DEX 0.000001272 0.53679 29.4372
102 1SR7 MOF 0.0000006023 0.58149 29.8701
103 4OAR 2S0 0.000001789 0.53201 29.8701
104 2Q1H AS4 0.00000002893 0.64075 32.9004
105 3DCT 064 0.0001776 0.44758 32.9004
106 3RUU 37G 0.0001527 0.47381 33.1878
107 5ICK FEZ 0.0007293 0.44847 33.1878
108 4S15 4D8 0.0008277 0.43801 33.7662
109 1N46 PFA 0.002528 0.40027 33.7662
110 3VRV YSD 0.0007868 0.46577 34.1991
111 4Q0A 4OA 0.001152 0.43979 34.632
112 4DK7 0KS 0.001435 0.43563 34.632
113 3L0E G58 0.0009004 0.41442 35.9307
114 5HCV 60R 0.0000000521 0.62169 36.3636
115 2A3I C0R 0.000000671 0.5676 36.3636
116 3KFC 61X 0.0001596 0.47941 36.3636
117 5L7G 6QE 0.00000001135 0.63411 36.7965
118 4UDB CV7 0.00000003793 0.59168 36.7965
119 1M13 HYF 0.004742 0.41486 37.2294
120 3G9E RO7 0.00002928 0.51263 38.5281
121 3FUR Z12 0.00007356 0.50982 38.5281
122 3V49 PK0 0.0000156 0.50956 38.5281
123 2AX9 BHM 0.000002089 0.43727 38.5281
124 5K13 6Q7 0.000115 0.46457 42.4242
125 3KMZ EQO 0.0002506 0.43167 42.4242
126 1U3R 338 0.0000000008436 0.71779 42.8571
127 1YYE 196 0.00000001679 0.57456 42.8571
128 4J26 EST 0.0000000159 0.56556 42.8571
129 4J24 EST 0.00000002509 0.56072 42.8571
130 2I0G I0G 0.00000006387 0.43892 42.8571
131 5TWO 7MV 0.0002533 0.46395 46.6667
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