Receptor
PDB id Resolution Class Description Source Keywords
1DKF 2.5 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAND-BINDING DOMAINS MUS MUSCULUS HELICAL SANDWICH HETERODIMER PROTEIN-LIGAND COMPLEX HORMONE/GROWTH FACTOR RECEPTOR STRUCTURAL PROTEOMICS IN EUROPE SPINE STRUCTURAL GENOMICS
Ref.: CRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAND-BINDING DOMAINS. MOL.CELL V. 5 289 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BMS B:600;
Valid;
none;
submit data
450.528 C29 H26 N2 O3 CC1(C...
OLA A:700;
Valid;
none;
submit data
282.461 C18 H34 O2 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DKF 2.5 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAND-BINDING DOMAINS MUS MUSCULUS HELICAL SANDWICH HETERODIMER PROTEIN-LIGAND COMPLEX HORMONE/GROWTH FACTOR RECEPTOR STRUCTURAL PROTEOMICS IN EUROPE SPINE STRUCTURAL GENOMICS
Ref.: CRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAND-BINDING DOMAINS. MOL.CELL V. 5 289 2000
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 1DKF - OLA C18 H34 O2 CCCCCCCCC=....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 1DKF - OLA C18 H34 O2 CCCCCCCCC=....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 1DKF - OLA C18 H34 O2 CCCCCCCCC=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BMS; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 BMS 1 1
2 EQN 0.414894 0.857143
Ligand no: 2; Ligand: OLA; Similar ligands found: 51
No: Ligand ECFP6 Tc MDL keys Tc
1 NER 1 1
2 OLA 1 1
3 ELA 1 1
4 PAM 0.939394 1
5 VCA 0.939394 1
6 MYZ 0.852941 0.954545
7 EIC 0.725 0.956522
8 STE 0.71875 0.954545
9 MYR 0.71875 0.954545
10 F23 0.71875 0.954545
11 DAO 0.71875 0.954545
12 11A 0.71875 0.954545
13 TDA 0.71875 0.954545
14 KNA 0.71875 0.954545
15 F15 0.71875 0.954545
16 DKA 0.71875 0.954545
17 DCR 0.71875 0.954545
18 PLM 0.71875 0.954545
19 OCA 0.6875 0.954545
20 ODD 0.675 0.956522
21 RCL 0.625 0.88
22 LNL 0.613636 0.869565
23 SHV 0.606061 0.909091
24 KTC 0.605263 0.84
25 3X1 0.564103 0.863636
26 ODT 0.555556 0.826087
27 T25 0.54717 0.709677
28 AZ1 0.53125 0.615385
29 6NA 0.529412 0.863636
30 10Y 0.529412 0.645161
31 10X 0.529412 0.645161
32 243 0.519231 0.846154
33 OLC 0.519231 0.617647
34 OLB 0.519231 0.617647
35 MVC 0.490566 0.617647
36 ACD 0.488889 0.956522
37 VA 0.478261 0.692308
38 3LA 0.47619 0.769231
39 78N 0.471698 0.617647
40 78M 0.471698 0.617647
41 EOD 0.468085 0.677419
42 MPG 0.45283 0.617647
43 14V 0.444444 0.714286
44 LEA 0.441176 0.772727
45 T24 0.438596 0.769231
46 BRC 0.435897 0.64
47 14U 0.431818 0.678571
48 M12 0.428571 0.833333
49 UNA 0.421053 0.636364
50 8YP 0.421053 0.636364
51 OCD 0.421053 0.636364
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1DKF; Ligand: BMS; Similar sites found: 138
This union binding pocket(no: 1) in the query (biounit: 1dkf.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TMX HGX 0.003055 0.41421 2.12766
2 2ET1 GLV 0.02975 0.40269 2.98507
3 1J78 OLA 0.02695 0.41268 3.00429
4 1I0B PEL 0.004525 0.45673 3.43348
5 2WTN FER 0.006243 0.43178 3.43348
6 1T27 PCW 0.006309 0.42052 3.43348
7 3IX9 MTX 0.006547 0.41026 3.68421
8 5IF4 6AK 0.01175 0.40358 3.77358
9 2P1C GG3 0.0009159 0.44251 3.82979
10 5B4B LP5 0.003627 0.41715 3.82979
11 4WRI OKA 0.009849 0.40124 4.16667
12 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.002209 0.47231 4.25532
13 3B6C SDN 0.000219 0.51176 4.2735
14 4UCC ZKW 0.009694 0.41642 4.29185
15 4Q86 AMP 0.0113 0.40665 4.29185
16 3VHZ L2P GLC MAN SGA 0.01779 0.40134 4.29185
17 3IA4 MTX 0.006811 0.41695 4.32099
18 4MNS 2AX 0.006838 0.42348 4.40252
19 4NB5 2JT 0.005133 0.41141 4.67836
20 1TV5 N8E 0.002306 0.45776 4.72103
21 3LDW ZOL 0.002647 0.4257 4.72103
22 4ORM ORO 0.01097 0.42436 4.72103
23 4ORM FMN 0.01097 0.42436 4.72103
24 4ORM 2V6 0.01097 0.42436 4.72103
25 1TV5 A26 0.01997 0.4023 4.72103
26 3OGN 3OG 0.003701 0.42134 4.83871
27 3B9Z CO2 0.03017 0.41066 5.15021
28 3GXO MQA 0.01865 0.40779 5.53191
29 4XNV BUR 0.01163 0.43438 5.5794
30 2XMY CDK 0.023 0.40869 5.5794
31 4YV5 SVR 0.007695 0.45244 5.7377
32 2VWA PTY 0.02997 0.40396 5.94059
33 3G5N PB2 0.02112 0.41775 5.95745
34 1P0H ACO 0.01003 0.42618 6.00858
35 5LX9 OLB 0.006446 0.41807 6.00858
36 3WYJ H78 0.01689 0.4156 6.00858
37 1XM4 PIL 0.002281 0.44375 6.38298
38 1XMU ROF 0.00423 0.42663 6.38298
39 4UBS DIF 0.02201 0.41341 6.38298
40 1L0I PSR 0.03339 0.40502 6.41026
41 3QCP FAD 0.005209 0.40617 6.43777
42 4HBM 0Y7 0.00299 0.40197 6.66667
43 4XPL ACO 0.01054 0.40099 6.74847
44 4LWU 20U 0.0014 0.44907 7.05882
45 5KAX RHQ 0.02405 0.40634 7.22892
46 4WT2 3UD 0.001112 0.43742 7.61905
47 4X6F 3XU 0.004486 0.42405 7.61905
48 4OGN 2U5 0.002213 0.40141 7.61905
49 5IBE 69M 0.009768 0.40709 7.65957
50 4IBF 1D5 0.005106 0.42281 7.75194
51 5U98 1KX 0.01476 0.41507 8.08081
52 4OKD GLC GLC GLC 0.02728 0.40874 8.15451
53 3L9R L9Q 0.006032 0.41283 8.16327
54 5L2J 70E 0.02492 0.40886 8.16327
55 5L2J 6UL 0.02351 0.40886 8.16327
56 5DCH 1YO 0.009957 0.4296 8.33333
57 3W54 RNB 0.003357 0.42323 8.58369
58 2QQC AG2 0.03072 0.40354 8.92857
59 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.004174 0.42849 9
60 4B1V LAB 0.01311 0.41132 9.3617
61 4B1X LAB 0.0179 0.40869 9.3617
62 3TDC 0EU 0.000407 0.50442 9.78723
63 1DMH LIO 0.01012 0.41045 9.87124
64 3MBG FAD 0.005643 0.40472 10.0719
65 2CB8 MYA 0.02517 0.40897 10.3448
66 4F4S EFO 0.002685 0.45564 10.5263
67 1NF8 BOG 0.0003668 0.50941 10.628
68 1EX7 5GP 0.008789 0.42904 10.7527
69 4DXJ IPE 0.003814 0.41891 11.1588
70 4DXJ 0M9 0.003651 0.41703 11.1588
71 5ECP MET 0.01498 0.40286 11.1588
72 4OAS 2SW 0.001315 0.45034 11.4583
73 5OCA 9QZ 0.0001117 0.56668 11.4894
74 4IGH 1EA 0.02217 0.41066 12.0172
75 4IGH ORO 0.02217 0.41066 12.0172
76 4IGH FMN 0.02217 0.41066 12.0172
77 1XVB 3BR 0.004735 0.43305 14.1176
78 3KO0 TFP 0.01298 0.41013 16.8317
79 3L1N PLM 0.01475 0.41738 17.0103
80 3SDV 911 0.01447 0.4016 17.0213
81 4I67 G G G RPC 0.00397 0.43681 17.2414
82 2X5W K2B 0.001523 0.4067 18.2979
83 3G08 FEE 0.02585 0.40104 18.8841
84 2V5E SCR 0.01251 0.4346 22.7723
85 1M2Z DEX 0.000001691 0.55703 27.0386
86 1M2Z BOG 0.0001465 0.55123 27.0386
87 4LSJ LSJ 0.000003289 0.52679 27.0386
88 1NHZ 486 0.000005248 0.52458 27.0386
89 5G5W R8C 0.000009481 0.52275 27.0386
90 3BQD DAY 0.000007492 0.51241 27.0386
91 4P6W MOF 0.00001055 0.5121 27.0386
92 4P6X HCY 0.00000449 0.51486 27.897
93 5DEY 59T 0.02233 0.40252 28.0851
94 3RY9 1CA 0.000006691 0.54378 29.1845
95 4E2J MOF 0.000004227 0.52844 29.1845
96 5UFS 1TA 0.000004553 0.52711 29.1845
97 3GN8 DEX 0.000008659 0.52668 29.1845
98 4OAR 2S0 0.0000000609 0.58825 29.6137
99 1SR7 MOF 0.0000006438 0.58025 29.6137
100 2Q1H AS4 0.00001826 0.486 32.618
101 2A3I C0R 0.000002749 0.52994 36.0515
102 5HCV 60R 0.00003261 0.50205 36.0515
103 5L7G 6QE 0.000001516 0.54674 36.4807
104 4UDB CV7 0.000004126 0.51156 36.4807
105 2AX9 BHM 0.0001273 0.49326 38.1974
106 3V49 PK0 0.000299 0.45625 38.1974
107 3DCT 064 0.00003414 0.49542 40
108 3BEJ MUF 0.00007824 0.47635 40
109 1M13 HYF 0.0001299 0.4817 40.4255
110 3SP6 IL2 0.0002592 0.43855 40.8511
111 3ET1 ET1 0.001585 0.4041 40.8511
112 5ICK FEZ 0.0001198 0.48274 41.048
113 3RUU 37G 0.00001597 0.46602 41.048
114 3KDU NKS 0.000689 0.46836 41.2017
115 2NPA MMB 0.002713 0.41637 41.2017
116 4J26 EST 0.000001491 0.59591 42.4893
117 2I0G I0G 0.000009213 0.55499 42.4893
118 1YYE 196 0.000001555 0.50745 42.4893
119 3OLL EST 0.000002718 0.50473 42.4893
120 1U3R 338 0.000006581 0.49803 42.4893
121 4J24 EST 0.000002197 0.49061 42.4893
122 2YJD YJD 0.00002436 0.46974 42.4893
123 3FUR Z12 0.000268 0.48471 42.9787
124 3G9E RO7 0.0003479 0.4663 42.9787
125 2PRG BRL 0.0005665 0.42317 42.9787
126 2HFP NSI 0.005202 0.40305 42.9787
127 4OIV XX9 0.00005125 0.50934 44.6903
128 5TWO 7MV 0.0005212 0.43197 46.6667
129 3IPQ 965 0.0000001715 0.5217 47.234
130 4DK7 0KS 0.00001826 0.51843 47.234
131 5LGA 6VH 0.00003137 0.51289 47.234
132 5E7V M7E 0.00003931 0.50047 47.234
133 4Q0A 4OA 0.0009214 0.44403 47.234
134 3KFC 61X 0.0000006594 0.58175 48.9362
135 5IXK 6EW 0.00307 0.40376 49.1228
136 3L0E G58 0.0000003808 0.58137 49.3617
137 4ZOM 4Q3 0.00003581 0.5458 49.7778
138 4S15 4D8 0.003977 0.4094 49.7872
Pocket No.: 2; Query (leader) PDB : 1DKF; Ligand: OLA; Similar sites found: 119
This union binding pocket(no: 2) in the query (biounit: 1dkf.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4I4B 1CV 0.01907 0.41014 2.57511
2 3AQT RCO 0.0004408 0.40731 2.57511
3 1NP7 FAD 0.0165 0.40739 3.00429
4 3QCQ 3Q0 0.0246 0.4338 3.40426
5 2ZKJ ADP 0.02696 0.40668 3.40426
6 3HYW DCQ 0.007138 0.42952 3.43348
7 1XON PIL 0.01185 0.41301 3.43348
8 1I0B PEL 0.01405 0.41202 3.43348
9 1T27 PCW 0.02923 0.40763 3.43348
10 5A8E XTK 0.01494 0.4025 3.43348
11 3OJI PYV 0.0103 0.40514 3.7037
12 3Q8G PEE 0.02859 0.41592 3.86266
13 5JNN 6LM 0.006629 0.41915 4.21053
14 4ZW9 BGC 0.006851 0.40951 4.25532
15 4ZW9 GLC 0.006851 0.40951 4.25532
16 1D4D FAD 0.02997 0.40877 4.25532
17 2ZCQ B65 0.02913 0.40856 4.25532
18 4UCC ZKW 0.002901 0.42216 4.29185
19 5JO1 6LM 0.005599 0.4174 4.68085
20 1TV5 N8E 0.01267 0.41948 4.72103
21 3KJS DQ1 0.02276 0.41222 4.72103
22 3B9Z CO2 0.003697 0.45257 5.15021
23 3WCA FPS 0.00428 0.43277 5.15021
24 4XRZ SI6 0.008544 0.41066 5.15021
25 2A1L PCW 0.006999 0.43978 5.53191
26 3JRS A8S 0.00456 0.41549 5.76923
27 4XT2 43L 0.01074 0.40768 5.78512
28 3KDJ A8S 0.003642 0.4241 5.94059
29 2VWA PTY 0.01018 0.42341 5.94059
30 4KCF AKM 0.00886 0.41322 6.00858
31 2EVL GAL SPH EIC 0.03928 0.40805 6.2201
32 3GWT 066 0.01761 0.40846 6.38298
33 3CV2 COA 0.01771 0.40708 6.38298
34 4UBS DIF 0.01601 0.40693 6.38298
35 4RW3 TDA 0.01979 0.42479 6.43777
36 4OIC A8S 0.005681 0.41115 6.76329
37 4TWP AXI 0.0269 0.41032 6.86695
38 4B7P 9UN 0.0123 0.42923 6.95652
39 4WZV E40 0.01328 0.40644 7.5
40 3RET SAL 0.004844 0.41208 7.92079
41 3RET PYR 0.004844 0.41208 7.92079
42 3NMV PYV 0.007188 0.40651 8.08511
43 4MOP 2H5 0.04957 0.40346 8.08511
44 5DLY 5D7 0.01721 0.41739 8.15451
45 3EKK GS2 0.02678 0.40389 8.15451
46 5L2J 70E 0.02485 0.42616 8.16327
47 5L2J 6UL 0.02359 0.42616 8.16327
48 4DS8 A8S 0.005587 0.40928 8.61244
49 3TL1 JRO 0.005279 0.42875 8.80503
50 4NKW PLO 0.003409 0.42542 9.3617
51 3LE7 ADE 0.02123 0.40223 9.78723
52 2Q2Y ADP 0.00427 0.44651 9.87124
53 2Q2Y MKR 0.004062 0.44651 9.87124
54 4J7Q B7N 0.02781 0.40205 9.87124
55 3RI1 3RH 0.009643 0.41731 10.2128
56 3KRR DQX 0.04126 0.41213 11.1588
57 5OCA 9QZ 0.002691 0.46282 11.4894
58 1W96 S1A 0.007659 0.4073 11.588
59 2Z7I 742 0.03377 0.41966 11.9149
60 1GEG GLC 0.008724 0.42511 13.1915
61 1N8V BDD 0.01402 0.41446 13.3929
62 3WV1 WHH 0.03662 0.40433 13.4503
63 2WCJ M21 0.007131 0.41602 13.4752
64 1XVB 3BR 0.001918 0.43982 14.1176
65 3R1V AZB 0.01261 0.4075 14.1732
66 5CSD ACD 0.02124 0.40888 14.4654
67 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.02642 0.40418 14.5923
68 5V4R MGT 0.01992 0.41207 14.8148
69 3KO0 TFP 0.01074 0.41146 16.8317
70 3G08 FEE 0.02485 0.41907 18.8841
71 4W9N TCL 0.01576 0.40494 22.7468
72 3BQD DAY 0.0000008468 0.5966 27.0386
73 5G5W R8C 0.000003408 0.58017 27.0386
74 1NHZ 486 0.000004014 0.56773 27.0386
75 4LSJ LSJ 0.000005447 0.55908 27.0386
76 1M2Z DEX 0.00000417 0.50588 27.0386
77 4P6W MOF 0.00002644 0.45702 27.0386
78 4P6X HCY 0.000007238 0.5508 27.897
79 3RY9 1CA 0.00000236 0.5374 29.1845
80 3GN8 DEX 0.000003902 0.50539 29.1845
81 5UFS 1TA 0.000005732 0.48187 29.1845
82 4E2J MOF 0.00000529 0.48177 29.1845
83 1SR7 MOF 0.000003031 0.59053 29.6137
84 4OAR 2S0 0.000001146 0.58775 29.6137
85 2Q1H AS4 0.0000007097 0.59442 32.618
86 2A3I C0R 0.0000006804 0.60101 36.0515
87 5HCV 60R 0.0000007573 0.5357 36.0515
88 5L7G 6QE 0.0000001212 0.63867 36.4807
89 4UDB CV7 0.0000009348 0.49546 36.4807
90 2AX9 BHM 0.000006434 0.58759 38.1974
91 3V49 PK0 0.000007683 0.55915 38.1974
92 3DCT 064 0.0001143 0.50389 40
93 3BEJ MUF 0.0002882 0.48112 40
94 1M13 HYF 0.007163 0.42745 40.4255
95 3SP6 IL2 0.00446 0.42005 40.8511
96 3ET1 ET1 0.009114 0.40576 40.8511
97 5ICK FEZ 0.001116 0.41932 41.048
98 3RUU 37G 0.00007907 0.40985 41.048
99 3KDU NKS 0.001516 0.47697 41.2017
100 3FEI CTM 0.01626 0.40077 41.2017
101 4J26 EST 0.00000003972 0.65089 42.4893
102 2I0G I0G 0.0000009032 0.64257 42.4893
103 2YJD YJD 0.0000001047 0.62578 42.4893
104 1YYE 196 0.0000001048 0.62208 42.4893
105 3OLL EST 0.0000001314 0.62131 42.4893
106 4J24 EST 0.00000006838 0.61906 42.4893
107 1U3R 338 0.0000003458 0.60559 42.4893
108 3G9E RO7 0.001501 0.46297 42.9787
109 3FUR Z12 0.003002 0.46014 42.9787
110 2PRG BRL 0.01026 0.40149 42.9787
111 2HFP NSI 0.01678 0.40012 42.9787
112 5TWO 7MV 0.009344 0.4071 46.6667
113 5LGA 6VH 0.001367 0.46623 47.234
114 5E7V M7E 0.001342 0.4598 47.234
115 3OKI OKI 0.002104 0.40049 48.0687
116 3KFC 61X 0.000332 0.49344 48.9362
117 5IXK 6EW 0.00387 0.42482 49.1228
118 3L0E G58 0.0004691 0.47846 49.3617
119 4ZOM 4Q3 0.0005365 0.51697 49.7778
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