Receptor
PDB id Resolution Class Description Source Keywords
1OPB 1.9 Å NON-ENZYME: TRANSPORT THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II RATTUS RATTUS RETINOL TRANSPORT
Ref.: CRYSTAL STRUCTURES OF HOLO AND APO-CELLULAR RETINOL-BINDING PROTEIN II. J.MOL.BIOL. V. 230 1247 1993
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
RET A:134;
B:134;
C:134;
D:134;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 50 nM
284.436 C20 H28 O CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1OPB 1.9 Å NON-ENZYME: TRANSPORT THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II RATTUS RATTUS RETINOL TRANSPORT
Ref.: CRYSTAL STRUCTURES OF HOLO AND APO-CELLULAR RETINOL-BINDING PROTEIN II. J.MOL.BIOL. V. 230 1247 1993
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 1OPB Kd = 50 nM RET C20 H28 O CC1=C(C(CC....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 families.
1 1OPB Kd = 50 nM RET C20 H28 O CC1=C(C(CC....
2 4QZU Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
3 4QYN Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
4 2RCT - RTL C20 H30 O CC1=C(C(CC....
5 4QZT Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
6 1KQW - RTL C20 H30 O CC1=C(C(CC....
50% Homology Family (104)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 1G74 Kd = 0.3 uM OLA C18 H34 O2 CCCCCCCCC=....
2 3FR5 ic50 = 0.069 uM I4A C22 H22 N2 O3 c1cc(cc(c1....
3 1LIE - PPI C3 H6 O2 CCC(=O)O
4 3FR4 ic50 = 0.049 uM F8A C21 H18 F3 N O2 c1ccc(c(c1....
5 2HNX - PLM C16 H32 O2 CCCCCCCCCC....
6 1ADL Kd = 4.4 uM ACD C20 H32 O2 CCCCCC=C/C....
7 5EDB Ki = 0.1 uM 5M8 C17 H12 Cl N O2 Cc1c(c(c2c....
8 1TOU ic50 = 1 uM B1V C12 H14 F3 N3 O2 S c1c(nc(nc1....
9 1LID - OLA C18 H34 O2 CCCCCCCCC=....
10 1LIF - STE C18 H36 O2 CCCCCCCCCC....
11 3JSQ - HNE C9 H16 O2 CCCCC[C@H]....
12 1TOW ic50 = 0.57 uM CRZ C16 H15 N O2 c1ccc2c(c1....
13 5EDC Ki = 0.022 uM 5M7 C21 H19 Cl N2 O2 c1ccc(cc1)....
14 5HZ8 Ki = 0.016 uM 65Z C21 H18 Cl2 N2 O2 c1ccc(cc1)....
15 3HK1 Ki = 0.67 uM B64 C14 H11 N O5 S2 COC(=O)c1c....
16 1LIC - PPI C3 H6 O2 CCC(=O)O
17 2NNQ Ki < 2 nM T4B C31 H26 N2 O3 CCc1c(c(nn....
18 3FR2 ic50 = 0.59 uM 8CA C20 H19 N O2 c1ccc(cc1)....
19 2ANS Kd = 1.2 uM 2AN C16 H13 N O3 S c1ccc(cc1)....
20 5HZ6 Ki = 0.016 uM 65Y C22 H22 Cl N O2 CC(C)c1ccc....
21 5L8N Kd = 31 uM 6RQ C9 H11 N3 Cc1cc2c(cc....
22 3WBG - 2AN C16 H13 N O3 S c1ccc(cc1)....
23 5HZ5 Ki = 0.086 uM 65X C21 H19 Cl N6 c1ccc(cc1)....
24 5UR9 Ki = 0.9 uM 8KS C28 H22 O4 c1ccc(cc1)....
25 1B56 - PLM C16 H32 O2 CCCCCCCCCC....
26 5D4A - 57Q C17 H15 N O2 c1ccc(cc1)....
27 5D47 Ki = 0.1 uM L19 C26 H24 N2 O3 COc1cnccc1....
28 5D48 Ki = 0.03 uM L96 C28 H31 N3 O3 Cc1c(c(n[n....
29 5D45 Ki = 0.12 uM 57P C26 H23 N O2 c1ccc(cc1)....
30 5URA Ki = 0.4 uM 8KS C28 H22 O4 c1ccc(cc1)....
31 1FDQ Kd = 53.4 nM HXA C22 H32 O2 CCC=C/CC=C....
32 2G78 - REA C20 H28 O2 CC1=C(C(CC....
33 2CBS Ki = 6 nM R13 C23 H30 O2 CC(=C/C(=O....
34 1CBS - REA C20 H28 O2 CC1=C(C(CC....
35 2FR3 Kd = 2 nM REA C20 H28 O2 CC1=C(C(CC....
36 3CWK Kd = 250 nM REA C20 H28 O2 CC1=C(C(CC....
37 3CBS Ki = 58 nM R12 C20 H24 O3 Cc1cc(c(c(....
38 2G79 Kd = 120 nM RET C20 H28 O CC1=C(C(CC....
39 2G7B - AZE C20 H30 CC=C(/C)C=....
40 1CBQ - RE9 C20 H28 O2 CC(=C/C(=O....
41 4TKB - DAO C12 H24 O2 CCCCCCCCCC....
42 4TJZ - DKA C10 H20 O2 CCCCCCCCCC....
43 1HMT Kd = 1.64 uM STE C18 H36 O2 CCCCCCCCCC....
44 4TKJ - PLM C16 H32 O2 CCCCCCCCCC....
45 5HZ9 Ki = 0.093 uM 5M8 C17 H12 Cl N O2 Cc1c(c(c2c....
46 4WBK - STE C18 H36 O2 CCCCCCCCCC....
47 3WVM - STE C18 H36 O2 CCCCCCCCCC....
48 4TKH - MYR C14 H28 O2 CCCCCCCCCC....
49 1HMR Kd = 0.28 uM ELA C18 H34 O2 CCCCCCCCC=....
50 1HMS Kd = 0.43 uM OLA C18 H34 O2 CCCCCCCCC=....
51 2HMB - PLM C16 H32 O2 CCCCCCCCCC....
52 3VG3 - PLM C16 H32 O2 CCCCCCCCCC....
53 3B2H - PLM C16 H32 O2 CCCCCCCCCC....
54 3B2K - PLM C16 H32 O2 CCCCCCCCCC....
55 3VG6 - PLM C16 H32 O2 CCCCCCCCCC....
56 3VG5 - PLM C16 H32 O2 CCCCCCCCCC....
57 3VG7 - PLM C16 H32 O2 CCCCCCCCCC....
58 3STM - PLM C16 H32 O2 CCCCCCCCCC....
59 3VG2 - PLM C16 H32 O2 CCCCCCCCCC....
60 3B2I - PLM C16 H32 O2 CCCCCCCCCC....
61 3B2L - PLM C16 H32 O2 CCCCCCCCCC....
62 3B2J - PLM C16 H32 O2 CCCCCCCCCC....
63 3VG4 - PLM C16 H32 O2 CCCCCCCCCC....
64 2WUT - PLM C16 H32 O2 CCCCCCCCCC....
65 4BVM - PLM C16 H32 O2 CCCCCCCCCC....
66 4D6B - PLM C16 H32 O2 CCCCCCCCCC....
67 5N4Q - PLM C16 H32 O2 CCCCCCCCCC....
68 4D6A - PLM C16 H32 O2 CCCCCCCCCC....
69 5N4P - PLM C16 H32 O2 CCCCCCCCCC....
70 5N4M - PLM C16 H32 O2 CCCCCCCCCC....
71 1OPB Kd = 50 nM RET C20 H28 O CC1=C(C(CC....
72 2Q9S - EIC C18 H32 O2 CCCCCC=C/C....
73 2QM9 Kd = 17 nM TDZ C24 H27 N O5 S Cc1c(c2c(c....
74 2QO4 - CHD C24 H40 O5 C[C@H](CCC....
75 2QO6 - CHD C24 H40 O5 C[C@H](CCC....
76 2QO5 - CHD C24 H40 O5 C[C@H](CCC....
77 1TW4 - CHD C24 H40 O5 C[C@H](CCC....
78 5BVT - PAM C16 H30 O2 CCCCCCC=C/....
79 3ELZ - CHD C24 H40 O5 C[C@H](CCC....
80 3EM0 - CHD C24 H40 O5 C[C@H](CCC....
81 4AZQ - G2A C23 H46 O4 CCCCCCCCCC....
82 4AZP Ki = 1.26 uM A9M C22 H45 N O2 CCCCCCCCCC....
83 5LJG - PLM C16 H32 O2 CCCCCCCCCC....
84 5LJC Kd = 65 nM RTL C20 H30 O CC1=C(C(CC....
85 5HBS Kd = 18.5 nM RTL C20 H30 O CC1=C(C(CC....
86 5H8T Kd = 18.5 nM RTL C20 H30 O CC1=C(C(CC....
87 5LJE Kd = 250 nM RTL C20 H30 O CC1=C(C(CC....
88 5LJD Kd = 70 nM RTL C20 H30 O CC1=C(C(CC....
89 5LJB Kd = 4.5 nM RTL C20 H30 O CC1=C(C(CC....
90 1CRB - RTL C20 H30 O CC1=C(C(CC....
91 5HA1 Kd = 64.1 nM RNE C20 H31 N CC1=C(C(CC....
92 4QZU Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
93 4QYN Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
94 2RCT - RTL C20 H30 O CC1=C(C(CC....
95 4QZT Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
96 1VYF Kd = 9 nM OLA C18 H34 O2 CCCCCCCCC=....
97 1VYG Kd = 10 nM ACD C20 H32 O2 CCCCCC=C/C....
98 2FT9 - CHD C24 H40 O5 C[C@H](CCC....
99 2FTB - OLA C18 H34 O2 CCCCCCCCC=....
100 1ICM - MYR C14 H28 O2 CCCCCCCCCC....
101 1ICN - OLA C18 H34 O2 CCCCCCCCC=....
102 2IFB Ki = 3.6 uM PLM C16 H32 O2 CCCCCCCCCC....
103 5BVS - EIC C18 H32 O2 CCCCCC=C/C....
104 1KQW - RTL C20 H30 O CC1=C(C(CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RET; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 RET 1 1
2 BCR 0.811321 0.863636
3 AZE 0.75 0.904762
4 9CR 0.704918 0.84
5 REA 0.704918 0.84
6 RNE 0.688525 0.655172
7 RTL 0.688525 0.740741
8 ECH 0.647059 0.84
9 ETR 0.641791 0.636364
10 RET RET 0.558442 0.826087
11 45D 0.455882 0.714286
12 6KX 0.425926 0.952381
13 EQ3 0.404762 0.666667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1OPB; Ligand: RET; Similar sites found: 48
This union binding pocket(no: 1) in the query (biounit: 1opb.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2X32 OTP 0.005772 0.43558 None
2 4QPW XYP XYP XYP 0.005572 0.41281 None
3 3RGA LSB 0.004206 0.41717 0.746269
4 4IAW LIZ 0.009349 0.41329 2.23881
5 3E9I XAH 0.01392 0.40097 2.23881
6 2XMY CDK 0.007716 0.44017 2.98507
7 3ZJX BOG 0.0103 0.42333 2.98507
8 2E56 MYR 0.008766 0.41134 2.98507
9 3KYF 5GP 5GP 0.01357 0.40545 2.98507
10 3L5R 47X 0.03185 0.41881 3.27869
11 1ULE GLA GAL NAG 0.0102 0.42469 3.73134
12 5IXH OTP 0.02394 0.40273 3.73134
13 4XMF HSM 0.002868 0.45065 4.47761
14 1C1L GAL BGC 0.007156 0.43345 4.47761
15 5HCY 60D 0.01414 0.41355 4.47761
16 3TAY MN0 0.009452 0.40585 4.47761
17 1ZQ5 E04 0.03213 0.40575 4.47761
18 1ZQ5 NAP 0.03213 0.40575 4.47761
19 2OVW CBI 0.01439 0.41284 5.22388
20 4I54 1C1 0.009723 0.4093 5.22388
21 3L9R L9R 0.01687 0.40512 5.22388
22 2A1L PCW 0.005008 0.43575 5.97015
23 1REQ DCA 0.02407 0.40348 5.97015
24 1Y52 BTN 0.014 0.41376 6.34921
25 5DRB 5FJ 0.004772 0.43768 6.71642
26 5TVM PUT 0.005481 0.43746 7.05882
27 5U98 1KX 0.02316 0.40159 7.07071
28 3VHH VHH 0.03298 0.4052 7.31707
29 3G08 FEE 0.03099 0.40515 8.08081
30 3A5Z KAA 0.005476 0.41497 8.20895
31 3Q8G PEE 0.02777 0.40748 8.20895
32 5LGA 6VH 0.01411 0.4066 8.95522
33 1T27 PCW 0.02481 0.40198 8.95522
34 4YBN FAD 0.00313 0.43021 9.70149
35 5IXG OTP 0.02449 0.4048 9.70149
36 3QRC SCR 0.007039 0.42728 10.4478
37 2YMZ LAT 0.000849 0.46799 10.7692
38 2VDF OCT 0.00136 0.46604 11.194
39 2HZQ STR 0.0188 0.40902 13.4328
40 5ECP MET 0.02199 0.40357 13.4328
41 4MNS 2AX 0.03314 0.40007 14.1791
42 2YNE NHW 0.01702 0.4327 14.9254
43 2YNE YNE 0.01702 0.4327 14.9254
44 4A91 GLU 0.01195 0.41861 16.4179
45 4NG2 OHN 0.009713 0.40241 16.8142
46 3VQ2 LP4 LP5 MYR DAO 0.01081 0.41905 22.3881
47 1MDC PLM 0.003933 0.41647 46.2121
48 3STK PLM 0.00001395 0.4255 49.2424
Pocket No.: 2; Query (leader) PDB : 1OPB; Ligand: RET; Similar sites found: 28
This union binding pocket(no: 2) in the query (biounit: 1opb.bio3) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3MVH WFE 0.01916 0.40089 None
2 3RGA ILD 0.01421 0.40004 0.746269
3 3BF8 MLA 0.01401 0.41379 2.23881
4 1ZB6 DIN 0.0118 0.40953 2.23881
5 5ML3 DL3 0.007244 0.42922 2.98507
6 4TW7 37K 0.01323 0.40443 3.125
7 4UWJ MYA 0.01588 0.43175 4.47761
8 4UWJ 7L5 0.01588 0.43175 4.47761
9 3O0Q ADN 0.04267 0.40955 4.47761
10 3O0Q TTP 0.04157 0.40955 4.47761
11 3O0Q GDP 0.04267 0.40955 4.47761
12 2YG2 S1P 0.008906 0.40435 5.22388
13 2YKL NLD 0.002621 0.41148 5.97015
14 4H6B 10Y 0.0124 0.40348 5.97015
15 5F3I 5UJ 0.01867 0.42212 6.71642
16 4WW7 AMP 0.0068 0.41144 6.71642
17 5LI1 ANP 0.008571 0.40687 6.71642
18 4QTB 38Z 0.01732 0.40168 6.71642
19 5MY8 RXZ 0.01501 0.40044 6.71642
20 4B2Z P5S 0.01768 0.41146 7.46269
21 5HA0 LTD 0.01145 0.40736 8.95522
22 3LVW GSH 0.02629 0.40108 8.95522
23 5DQ8 FLF 0.01751 0.40398 9.70149
24 4YZC STU 0.02644 0.40095 10.4478
25 4IGQ THR M3L GLN 0.004462 0.41602 12.6866
26 3PE2 E1B 0.03082 0.40501 14.1791
27 4XT2 43L 0.01301 0.40024 15.7025
28 1WUB OTP 0.01287 0.42204 27.6119
Pocket No.: 3; Query (leader) PDB : 1OPB; Ligand: RET; Similar sites found: 10
This union binding pocket(no: 3) in the query (biounit: 1opb.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ZB6 GST 0.004611 0.41918 2.23881
2 5DMZ ADP 0.004772 0.40923 3.73134
3 1G9J BGC SGC BGC SGC BGC SGC BGC SGC 0.04557 0.40061 4.47761
4 1GZW GAL BGC 0.01288 0.41613 5.22388
5 5MRH Q9Z 0.01607 0.40776 5.22388
6 5BVE 4VG 0.01627 0.41931 6.71642
7 3A5Y KAA 0.008533 0.40014 8.20895
8 2VFT SOR 0.01029 0.41309 8.95522
9 3MTX PGT 0.002411 0.43437 9.70149
10 3FP0 FP0 0.007619 0.40042 11.194
Pocket No.: 4; Query (leader) PDB : 1OPB; Ligand: RET; Similar sites found: 9
This union binding pocket(no: 4) in the query (biounit: 1opb.bio4) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1O44 852 0.017 0.40906 None
2 1E1M FAD 0.03892 0.40373 3.73134
3 4WHZ 3NL 0.03587 0.4004 4.47761
4 5IH9 6BF 0.01314 0.41121 5.22388
5 1W6P NDG GAL 0.03091 0.40278 5.22388
6 3A7R LAQ 0.00544 0.43037 7.46269
7 3VRV YSD 0.02884 0.40585 8.95522
8 2E5A LAQ 0.003092 0.4328 9.70149
9 5UIU 8CG 0.01495 0.40269 9.70149
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