Receptor
PDB id Resolution Class Description Source Keywords
4LBD 2.5 Å NON-ENZYME: TRANSCRIPT_TRANSLATE LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO THE SYNTHETIC AGONIST BMS961 HOMO SAPIENS NUCLEAR RECEPTOR RETINOIC ACID RECEPTOR ALL-TRANS RETINOIC ACID LIGAND-BINDING DOMAIN COMPLEX HOLO FORM TRANSCRIPTION REGULATION LIGAND-DEPENDENT ACTIVE CONFORMATION STRUCTURAL PROTEOMICS IN EUROPE SPINE STRUCTURAL GENOMICS
Ref.: CONFORMATIONAL ADAPTATION OF AGONISTS TO THE HUMAN NUCLEAR RECEPTOR RAR GAMMA. NAT.STRUCT.BIOL. V. 5 199 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
961 A:1;
Valid;
none;
submit data
399.455 C23 H26 F N O4 CC1(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2LBD 2.06 Å NON-ENZYME: TRANSCRIPT_TRANSLATE LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO ALL-TRANS RETINOIC ACID HOMO SAPIENS NUCLEAR RECEPTOR RETINOIC ACID RECEPTOR ALL-TRANS RETINOIC ACID LIGAND-BINDING DOMAIN COMPLEX HOLO FORM TRANSCRIPTION REGULATION LIGAND-DEPENDENT ACTIVE CONFORMATION STRUCTURAL PROTEOMICS IN EUROPE SPINE STRUCTURAL GENOMICS
Ref.: CRYSTAL STRUCTURE OF THE RAR-GAMMA LIGAND-BINDING DOMAIN BOUND TO ALL-TRANS RETINOIC ACID. NATURE V. 378 681 1995
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 2LBD - REA C20 H28 O2 CC1=C(C(CC....
2 4LBD - 961 C23 H26 F N O4 CC1(CCC(c2....
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: 961; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 961 1 1
2 394 1 1
3 184 0.5 0.6
4 EQN 0.407407 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2LBD; Ligand: REA; Similar sites found: 134
This union binding pocket(no: 1) in the query (biounit: 2lbd.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5XNA SHV 0.01324 0.41654 None
2 5N8V KZZ 0.02319 0.40596 None
3 5DKK FMN 0.00851 0.40496 None
4 2Z6D FMN 0.01077 0.40041 None
5 2F2G HMH 0.01338 0.42537 0.904977
6 2Q4X HMH 0.02365 0.40895 0.904977
7 1QY8 RDI 0.003259 0.43112 1.49813
8 1H0A I3P 0.02631 0.41252 1.89873
9 1TV5 N8E 0.001587 0.47909 2.24719
10 1NE7 16G 0.008439 0.43312 2.24719
11 5CX8 TG6 0.02081 0.42044 2.24719
12 5LUN ARG 0.01305 0.41873 2.24719
13 3R9V DXC 0.01737 0.41836 2.24719
14 3KU0 ADE 0.02446 0.41114 2.39044
15 4JWK CTN 0.004352 0.4495 2.59067
16 3V1S 0LH 0.01298 0.41491 2.62172
17 2QES ADE 0.02981 0.40553 2.68199
18 2WTN FER 0.006705 0.43344 2.78884
19 3GUZ PAF 0.02702 0.40355 2.84091
20 3WXL ADP 0.004296 0.43889 2.89575
21 4XNV BUR 0.01359 0.42302 2.99625
22 3HYW DCQ 0.02309 0.40933 2.99625
23 5VRH OLB 0.03426 0.4042 2.99625
24 5EDE 5M6 0.02892 0.40104 2.99625
25 4P3H 25G 0.007855 0.4065 3.10881
26 5LX9 OLB 0.005056 0.42629 3.37079
27 5B25 4QJ 0.008456 0.41199 3.37079
28 4MRP GSH 0.02246 0.40487 3.37079
29 5CQG 55C 0.02589 0.41063 3.74532
30 2XUA SHF 0.0179 0.41611 3.7594
31 3HP9 CF1 0.01338 0.42581 4.11985
32 4D4U FUC NDG GAL FUC 0.03288 0.4034 4.49438
33 4UY1 TJM 0.01987 0.4054 4.58015
34 1N9L FMN 0.01002 0.4018 4.58716
35 3P2H MTA 0.02906 0.40715 4.86891
36 3ZJX BOG 0.03371 0.40283 4.86891
37 3KO0 TFP 0.01631 0.40653 4.9505
38 4CB5 93G 0.02011 0.40141 5.38922
39 3CYI ATP 0.02767 0.40823 5.45455
40 2QJY UQ2 0.01173 0.42566 5.88235
41 2WKQ FMN 0.007144 0.40832 5.99251
42 1YC4 43P 0.007968 0.42092 6.06061
43 5UC9 MYR 0.02822 0.40158 7.07965
44 1RL4 BL5 0.007414 0.42578 7.44681
45 5LWY OLB 0.0005601 0.47136 7.56302
46 5EFW FMN 0.004239 0.41836 7.58621
47 5DJT FMN 0.005806 0.41231 7.58621
48 5DJU FMN 0.008698 0.40133 7.58621
49 4RW3 DKA 0.002787 0.47869 7.86517
50 4RW3 PLM 0.02765 0.40719 7.86517
51 3G08 FEE 0.005256 0.42691 8.08081
52 3DBX PLM 0.01032 0.41549 8.08081
53 4RQL SNE 0.01841 0.41109 8.2397
54 3RDE OYP 0.00434 0.40794 8.2397
55 3SHZ 5CO 0.01809 0.40744 8.2397
56 2HFK E4H 0.03014 0.40413 8.2397
57 2P39 SCR 0.02494 0.40858 8.3871
58 3GXO MQA 0.01197 0.42063 8.98876
59 5J32 IPM 0.01596 0.42043 8.98876
60 2W9S TOP 0.02622 0.40733 9.31677
61 1A05 IPM 0.01194 0.42724 9.73783
62 3UP3 XCA 0.0008612 0.43355 10.2881
63 2V0U FMN 0.005921 0.41194 12.3288
64 3X27 TRP 0.03358 0.40226 12.7341
65 1M48 FRG 0.02492 0.40849 12.782
66 1SBR VIB 0.02223 0.4111 13
67 4RJD TFP 0.0105 0.41959 13.6364
68 2CB8 MYA 0.03138 0.40635 13.7931
69 1NHZ 486 0.0001806 0.47418 14.2322
70 5G5W R8C 0.00003578 0.47241 14.2322
71 3TDC 0EU 0.003755 0.41942 14.6067
72 4LSJ LSJ 0.00003889 0.4702 14.7287
73 1M2Z DEX 0.00001073 0.52721 14.786
74 1M2Z BOG 0.004857 0.45925 14.786
75 4P6X HCY 0.00002598 0.47185 14.902
76 3BQD DAY 0.00004349 0.4681 14.902
77 4P6W MOF 0.00005091 0.48821 15.0794
78 3RY9 1CA 0.0002717 0.47584 15.2
79 4E2J MOF 0.00002877 0.49851 15.6
80 3GN8 DEX 0.00004937 0.49854 15.6627
81 5UFS 1TA 0.0001178 0.47307 15.7258
82 3V49 PK0 0.0006145 0.43596 16.1654
83 4OAR 2S0 0.00000233 0.55588 20.5993
84 1SR7 MOF 0.00004064 0.49416 20.5993
85 5L7G 6QE 0.00004586 0.47265 21.3483
86 4UDB CV7 0.0001027 0.46705 21.3483
87 2Q1H AS4 0.0004381 0.46191 27.3408
88 5HCV 60R 0.0008554 0.44497 34.2412
89 2A3I C0R 0.00007004 0.48711 34.7826
90 1YYE 196 0.00004753 0.52185 34.8315
91 3SP6 IL2 0.002494 0.42854 36.3296
92 2P54 735 0.002476 0.40667 36.7041
93 5DXG EST 0.00001586 0.55128 37.4532
94 5DX3 EST 0.00001744 0.54929 37.4532
95 5DXE EST 0.00002252 0.53714 37.4532
96 3FUR Z12 0.0009621 0.45289 37.4532
97 3G9E RO7 0.0009786 0.43995 37.4532
98 5TWO 7MV 0.002526 0.42461 37.4532
99 2PRG BRL 0.005841 0.41572 37.4532
100 5HYR EST 0.00001552 0.54475 37.5969
101 4MG9 27K 0.00001341 0.57872 38.0392
102 4MGA 27L 0.00003074 0.56461 38.0392
103 4MGB XDH 0.00000357 0.56068 38.0392
104 4MG7 27H 0.000005821 0.5511 38.0392
105 4MGD 27N 0.00001675 0.5432 38.0392
106 4MG8 27J 0.00006031 0.51698 38.0392
107 4TUZ 36J 0.0001709 0.50148 38.0392
108 1U3R 338 0.0001409 0.48871 38.5892
109 3UUD EST 0.00001729 0.54254 38.6454
110 4TV1 36M 0.0001462 0.52478 38.6454
111 3UUA 0CZ 0.0001026 0.5186 38.6454
112 3UU7 2OH 0.000422 0.50085 38.6454
113 4J26 EST 0.00001715 0.54963 38.75
114 2YJD YJD 0.0002597 0.48177 38.75
115 3OLL EST 0.00005162 0.44568 38.75
116 3BEJ MUF 0.00002111 0.5041 39.0756
117 2R40 20E 0.0001282 0.4632 39.4737
118 3DCT 064 0.00004619 0.48094 39.5745
119 5IXK 6EW 0.002104 0.42805 39.9123
120 3OKI OKI 0.003786 0.417 39.9142
121 4ZOM 4Q3 0.002134 0.45573 40.4444
122 5ICK FEZ 0.0001236 0.48618 40.6114
123 3RUU 37G 0.00001507 0.48043 40.6114
124 5E7V M7E 0.0001063 0.47369 41.9476
125 4Q0A 4OA 0.0007231 0.4523 41.9476
126 5LGA 6VH 0.00002565 0.44422 41.9476
127 4J24 EST 0.00001725 0.45002 42.1053
128 3H0A 9RA 0.0002043 0.43215 42.5439
129 4DK7 0KS 0.000004234 0.55085 44.5344
130 3L0E G58 0.00000001935 0.59551 45.0593
131 4S15 4D8 0.00141 0.43183 45.3125
132 2O4J VD4 0.00008437 0.46025 47.9401
133 1RDT L79 0.0001611 0.47632 48.6891
134 1RDT 570 0.002296 0.41304 48.6891
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