Receptor
PDB id Resolution Class Description Source Keywords
2g79 1.69 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF THE R132K:Y134F MUTANT OF CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II IN COMPLEX WITH ALL- T RANS-RETINAL AT 1.69 ANGSTROMS RESOLUTION HOMO SAPIENS CRABPII RETINOIC ACID RETINOIDS BETA BARREL CRYSTALLOGRAPHY X-RAY HIGH RESOLUTION RETINAL TRANSPORTPROTEIN
Ref.: PROTEIN DESIGN: REENGINEERING CELLULAR RETINOIC ACID BINDING PROTEIN II INTO A RHODOPSIN PROTEIN MIMIC. J.AM.CHEM.SOC. V. 129 6140 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA A:300;
A:301;
A:302;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
22.99 Na [Na+]
RET A:200;
Valid;
none;
Kd = 120 nM
284.436 C20 H28 O CC1=C...
SO4 A:400;
A:401;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2FR3 1.48 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID AT 1.48 A NGSTROMS RESOLUTION HOMO SAPIENS CRABPII RETINOIC ACID RETINOIDS BETA BARREL CRYSTALLOGRAPHY X-RAY HIGH RESOLUTION TRANSPORT PROTEIN
Ref.: THE STRUCTURE OF APO-WILD-TYPE CELLULAR RETINOIC ACID BINDING PROTEIN II AT 1.4 A AND ITS RELATIONSHIP TO LIGAND BINDING AND NUCLEAR TRANSLOCATION. J.MOL.BIOL. V. 363 687 2006
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 2G78 - REA C20 H28 O2 CC1=C(C(CC....
2 2CBS Ki = 6 nM R13 C23 H30 O2 CC(=C/C(=O....
3 1CBS - REA C20 H28 O2 CC1=C(C(CC....
4 2FR3 Kd = 2 nM REA C20 H28 O2 CC1=C(C(CC....
5 3CWK Kd = 250 nM REA C20 H28 O2 CC1=C(C(CC....
6 3CBS Ki = 58 nM R12 C20 H24 O3 Cc1cc(c(c(....
7 2G79 Kd = 120 nM RET C20 H28 O CC1=C(C(CC....
8 2G7B - AZE C20 H30 CC=C(/C)C=....
9 1CBQ - RE9 C20 H28 O2 CC(=C/C(=O....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 2G78 - REA C20 H28 O2 CC1=C(C(CC....
2 2CBS Ki = 6 nM R13 C23 H30 O2 CC(=C/C(=O....
3 1CBS - REA C20 H28 O2 CC1=C(C(CC....
4 2FR3 Kd = 2 nM REA C20 H28 O2 CC1=C(C(CC....
5 3CWK Kd = 250 nM REA C20 H28 O2 CC1=C(C(CC....
6 3CBS Ki = 58 nM R12 C20 H24 O3 Cc1cc(c(c(....
7 2G79 Kd = 120 nM RET C20 H28 O CC1=C(C(CC....
8 2G7B - AZE C20 H30 CC=C(/C)C=....
9 1CBQ - RE9 C20 H28 O2 CC(=C/C(=O....
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 : 2FR3; Ligand: REA; Similar sites found: 13
This union binding pocket(no: 1) in the query (biounit: 2fr3.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZFZ ARG 0.02248 0.43356 None
2 2VWA PTY 0.01508 0.41696 None
3 3QVV A3P 0.01525 0.41108 4.37956
4 3QVV 3QV 0.01525 0.41108 4.37956
5 1LN1 DLP 0.00372 0.4308 5.10949
6 2A1L PCW 0.0158 0.41217 5.83942
7 1TV5 N8E 0.01912 0.41794 6.56934
8 3RUG DB6 0.0136 0.41785 8.08081
9 3G08 FEE 0.02324 0.41125 8.08081
10 4N9I PCG 0.03296 0.40095 9.48905
11 3HUJ AGH 0.02459 0.40553 10.219
12 1D6H COA 0.02372 0.40463 13.8686
13 1EWF PC1 0.01216 0.41475 15.3285
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