Receptor
PDB id Resolution Class Description Source Keywords
4DM8 2.3 Å EC: 2.3.1.48 CRYSTAL STRUCTURE OF RARB LBD IN COMPLEX WITH 9CIS RETINOIC HOMO SAPIENS NUCLEAR RECEPTOR RARB 9CIS RETINOIC ACID ALPHA HELICAL SATRANSCRIPTION FACTOR RETINOIC ACID TRANSCRIPTION-PROTEIN COMPLEX
Ref.: STRUCTURAL BASIS FOR A MOLECULAR ALLOSTERIC CONTROL MECHANISM OF COFACTOR BINDING TO NUCLEAR RECEPTORS. PROC.NATL.ACAD.SCI.USA V. 109 E588 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
REA A:501;
B:1501;
Valid;
Valid;
none;
none;
submit data
300.435 C20 H28 O2 CC1=C...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DM8 2.3 Å EC: 2.3.1.48 CRYSTAL STRUCTURE OF RARB LBD IN COMPLEX WITH 9CIS RETINOIC HOMO SAPIENS NUCLEAR RECEPTOR RARB 9CIS RETINOIC ACID ALPHA HELICAL SATRANSCRIPTION FACTOR RETINOIC ACID TRANSCRIPTION-PROTEIN COMPLEX
Ref.: STRUCTURAL BASIS FOR A MOLECULAR ALLOSTERIC CONTROL MECHANISM OF COFACTOR BINDING TO NUCLEAR RECEPTORS. PROC.NATL.ACAD.SCI.USA V. 109 E588 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 4DM8 - REA C20 H28 O2 CC1=C(C(CC....
2 4DM6 - TTB C24 H28 O2 C/C(=Cc1cc....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 30 families.
1 4DM8 - REA C20 H28 O2 CC1=C(C(CC....
2 4DM6 - TTB C24 H28 O2 C/C(=Cc1cc....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3KMR - EQN C22 H25 N O3 CC1(CCC(c2....
2 4DM8 - REA C20 H28 O2 CC1=C(C(CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: REA; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 REA 1 1
2 9CR 1 1
3 BCR 0.724138 0.730769
4 RET 0.704918 0.84
5 AZE 0.7 0.76
6 RTL 0.671875 0.758621
7 ECH 0.589041 0.724138
8 RET RET 0.512195 0.703704
9 45D 0.410959 0.677419
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DM8; Ligand: REA; Similar sites found: 95
This union binding pocket(no: 1) in the query (biounit: 4dm8.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.0008636 0.4706 None
2 1JGS SAL 0.01192 0.42244 None
3 5N8V KZZ 0.01502 0.41255 None
4 5LUN ARG 0.01431 0.4136 1.49813
5 4UY1 TJM 0.01296 0.41157 1.52672
6 3DCJ THH 0.008947 0.4077 1.86047
7 1TV5 N8E 0.01083 0.42435 2.24719
8 1QY8 RDI 0.00633 0.41458 2.62172
9 1AUA BOG 0.02151 0.40887 2.62172
10 2WTN FER 0.01695 0.4099 2.78884
11 5VRH OLB 0.02985 0.40445 3.06513
12 5CQG 55C 0.02882 0.40197 3.74532
13 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.04068 0.40014 4.11985
14 4WGF HX2 0.02155 0.41721 4.87805
15 4URG C2E 0.01083 0.42255 5.38922
16 4UBS DIF 0.01264 0.41897 5.61798
17 1NF8 BOG 0.004636 0.45108 6.28019
18 3A8H TAY 0.03322 0.40063 6.28019
19 2Q8H TF4 0.02487 0.41633 6.36704
20 3RV5 DXC 0.0001319 0.41755 6.74157
21 2QJY UQ2 0.01552 0.41737 6.74157
22 4RW3 TDA 0.04115 0.41219 8
23 1XZ3 ICF 0.01214 0.43332 8.04598
24 2CB8 MYA 0.02352 0.41033 8.04598
25 1XVB 3BR 0.004417 0.43453 8.2397
26 5J32 IPM 0.01247 0.42344 8.2397
27 4UCC ZKW 0.04455 0.40201 8.58369
28 1OW4 2AN 0.0185 0.40015 9.30233
29 1D6Z HY1 0.02564 0.40972 9.3633
30 3KP6 SAL 0.01527 0.42317 9.93377
31 2PYW SR1 0.005333 0.44177 10.1124
32 3UP3 XCA 0.001123 0.42309 10.2881
33 3GYT DL4 0.0001573 0.45687 11.0656
34 1RL4 BL5 0.01998 0.42584 11.985
35 3KO0 TFP 0.03929 0.40634 12
36 5G5W R8C 0.00002156 0.47216 14.2322
37 1NHZ 486 0.0006308 0.43909 14.2322
38 4LSJ LSJ 0.00003832 0.4842 14.7287
39 1M2Z DEX 0.00003429 0.50111 14.786
40 1M2Z BOG 0.003013 0.4805 14.786
41 4P6X HCY 0.0000661 0.47019 14.902
42 3TDC 0EU 0.001762 0.47179 14.9813
43 4P6W MOF 0.0002418 0.4562 15.0794
44 4E2J MOF 0.00008373 0.47514 15.6
45 3GN8 DEX 0.0001022 0.48082 15.6627
46 5UFS 1TA 0.0001492 0.46483 15.7258
47 2AX9 BHM 0.001011 0.45363 16.7969
48 3AQT RCO 0.0306 0.4012 20
49 4OAR 2S0 0.000004947 0.53708 20.5993
50 1SR7 MOF 0.0001315 0.48148 20.5993
51 5L7G 6QE 0.00003206 0.49227 22.0974
52 4UDB CV7 0.00007629 0.46399 22.0974
53 3V49 PK0 0.001072 0.4332 22.1805
54 5LWY OLB 0.0009964 0.45597 24
55 5LX9 OLB 0.004599 0.42493 24
56 5EWK P34 0.01237 0.42259 24
57 3RY9 1CA 0.0002272 0.47545 26.9663
58 1BRW URA 0.02701 0.40624 28
59 5KEW 6SB 0.02186 0.4043 28
60 2Q1H AS4 0.0004026 0.43506 30
61 1YMT DR9 0.0002361 0.46582 30.8943
62 1YP0 PEF 0.001002 0.43083 31.3808
63 3SHZ 5CO 0.0152 0.40815 32
64 2XN5 FUN 0.02027 0.40198 32
65 1ZDT PEF 0.0002029 0.43657 32.2097
66 4QJR PIZ 0.0003237 0.43438 32.2097
67 1G2N EPH 0.005009 0.40374 37.1212
68 1HG4 LPP 0.004605 0.40991 37.276
69 3FUR Z12 0.00074 0.46498 38.2022
70 5TWO 7MV 0.007466 0.40102 38.2022
71 1YOK P6L 0.00002039 0.52253 39.0625
72 4J26 EST 0.000002521 0.58501 39.1667
73 2E2R 2OH 0.00003317 0.51184 40.1639
74 2O4J VD4 0.00003137 0.46833 40.4494
75 3OKI OKI 0.007036 0.40212 40.7725
76 5UNJ RJW 0.0006823 0.45877 40.8163
77 2R40 20E 0.000002491 0.51849 41.1985
78 3FS1 MYR 0.0002695 0.42885 41.3043
79 4Q0A 4OA 0.0009237 0.44399 42.3221
80 1FBY REA 0.0001167 0.46234 43.0962
81 5GIC DLC 0.00008793 0.48565 43.2
82 5OCA 9QZ 0.009932 0.43269 44
83 1N46 PFA 0.000002046 0.54851 45.3488
84 1YUC EPH 0.001086 0.41771 45.4902
85 1DB1 VDX 0.00005908 0.49793 45.5598
86 3JZB 4HY 0.0000036 0.49465 45.6929
87 3KFC 61X 0.0000001052 0.61598 45.8498
88 3L0E G58 0.00000003912 0.62286 46.2451
89 1N83 CLR 0.002547 0.41757 46.6667
90 5X8Q 82R 0.002949 0.40081 46.8992
91 4S15 4D8 0.000448 0.44919 47.2656
92 5IXK 6EW 0.004978 0.40857 48.2456
93 1NQ7 ARL 0.003108 0.41734 48.7705
94 4ZOM 4Q3 0.001108 0.47559 48.8889
95 3VRV YSD 0.0000785 0.51079 49.0637
Pocket No.: 2; Query (leader) PDB : 4DM8; Ligand: REA; Similar sites found: 18
This union binding pocket(no: 2) in the query (biounit: 4dm8.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.008275 0.43452 None
2 2ZCQ B65 0.02027 0.40142 2.62172
3 3GUZ PAF 0.01852 0.40921 3.40909
4 2J7T 274 0.008204 0.40504 3.74532
5 1L0I PSR 0.03073 0.40546 3.84615
6 4Q3F TLA 0.0318 0.40052 4.2735
7 4D4U FUC NDG GAL FUC 0.02479 0.40684 4.49438
8 1R6N 434 0.02157 0.40808 4.73934
9 4BWL MN9 0.01565 0.41677 4.86891
10 3SDV 911 0.0144 0.40007 7.49064
11 3GXO MQA 0.007743 0.42538 8.61423
12 3P2H MTA 0.01898 0.40677 8.61423
13 1A05 IPM 0.009915 0.42708 9.3633
14 5UC9 MYR 0.01976 0.41008 13.2743
15 3L1N PLM 0.01835 0.41086 13.8577
16 5CX8 TG6 0.02729 0.40634 24
17 3R9V DXC 0.02583 0.40557 32
18 3D91 REM 0.03593 0.40139 36
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