Receptor
PDB id Resolution Class Description Source Keywords
5LJB 1.26 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF HOLO HUMAN CRBP1 HOMO SAPIENS RETINOL VITAMIN A RETINOL-BINDING PROTEIN RBP
Ref.: STRUCTURAL AND MOLECULAR DETERMINANTS AFFECTING THE INTERACTION OF RETINOL WITH HUMAN CRBP1. J. STRUCT. BIOL. V. 197 330 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
RTL A:201;
Valid;
none;
Kd = 4.5 nM
286.452 C20 H30 O CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LJB 1.26 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF HOLO HUMAN CRBP1 HOMO SAPIENS RETINOL VITAMIN A RETINOL-BINDING PROTEIN RBP
Ref.: STRUCTURAL AND MOLECULAR DETERMINANTS AFFECTING THE INTERACTION OF RETINOL WITH HUMAN CRBP1. J. STRUCT. BIOL. V. 197 330 2017
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 5LJG - PLM C16 H32 O2 CCCCCCCCCC....
2 5LJC Kd = 65 nM RTL C20 H30 O CC1=C(C(CC....
3 5HBS Kd = 18.5 nM RTL C20 H30 O CC1=C(C(CC....
4 5H8T Kd = 18.5 nM RTL C20 H30 O CC1=C(C(CC....
5 5LJE Kd = 250 nM RTL C20 H30 O CC1=C(C(CC....
6 5LJD Kd = 70 nM RTL C20 H30 O CC1=C(C(CC....
7 5LJB Kd = 4.5 nM RTL C20 H30 O CC1=C(C(CC....
8 1CRB - RTL C20 H30 O CC1=C(C(CC....
9 5HA1 Kd = 64.1 nM RNE C20 H31 N CC1=C(C(CC....
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 5LJG - PLM C16 H32 O2 CCCCCCCCCC....
2 5LJC Kd = 65 nM RTL C20 H30 O CC1=C(C(CC....
3 5HBS Kd = 18.5 nM RTL C20 H30 O CC1=C(C(CC....
4 5H8T Kd = 18.5 nM RTL C20 H30 O CC1=C(C(CC....
5 5LJE Kd = 250 nM RTL C20 H30 O CC1=C(C(CC....
6 5LJD Kd = 70 nM RTL C20 H30 O CC1=C(C(CC....
7 5LJB Kd = 4.5 nM RTL C20 H30 O CC1=C(C(CC....
8 1CRB - RTL C20 H30 O CC1=C(C(CC....
9 5HA1 Kd = 64.1 nM RNE C20 H31 N 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: RTL; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 RTL 1 1
2 RNE 0.766667 0.709677
3 BCR 0.736842 0.703704
4 AZE 0.711864 0.730769
5 RET 0.688525 0.740741
6 REA 0.671875 0.758621
7 9CR 0.671875 0.758621
8 ETR 0.614286 0.638889
9 OXR 0.57971 0.774194
10 ECH 0.575342 0.645161
11 RET RET 0.518519 0.678571
12 3ON 0.417722 0.71875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5LJB; Ligand: RTL; Similar sites found: 64
This union binding pocket(no: 1) in the query (biounit: 5ljb.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3Q8U ADP 0.01892 0.40897 None
2 4RT1 C2E 0.007509 0.40771 None
3 4H6B 10X 0.01503 0.40118 None
4 3RG9 WRA 0.01426 0.40753 0.740741
5 1A78 TDG 0.01292 0.42083 1.49254
6 1OGX EQU 0.005614 0.41734 1.52672
7 5IXH OTP 0.008695 0.42031 2.22222
8 3VV1 GAL FUC 0.01638 0.41429 2.22222
9 2YMZ LAT 0.007806 0.40844 2.30769
10 3A76 SPD 0.01224 0.41902 2.96296
11 4FFG 0U8 0.01668 0.41351 2.96296
12 4BPZ GLC BGC BGC 0.01496 0.40931 2.96296
13 4MPO AMP 0.01374 0.40155 2.96296
14 2VDF OCT 0.004578 0.4292 3.7037
15 5ML3 DL3 0.01223 0.40855 3.7037
16 1P0Z FLC 0.02404 0.40633 3.81679
17 4B1L FRU 0.008564 0.43741 4.44444
18 5EW9 5VC 0.02257 0.42942 4.44444
19 3MTX PGT 0.003834 0.4254 4.44444
20 3KYG 5GP 5GP 0.00666 0.41007 4.44444
21 3RGA LSB 0.001822 0.40824 4.44444
22 4XBT 3ZQ 0.01086 0.40788 4.44444
23 5IXG OTP 0.02175 0.40442 4.44444
24 2A1L PCW 0.02083 0.40361 4.44444
25 4WVW SLT 0.02255 0.4027 4.44444
26 5LUN OGA 0.02598 0.40139 4.44444
27 3NRR D16 0.02769 0.40109 4.44444
28 4IAW LIZ 0.001081 0.46059 5.18518
29 1NSZ GLC 0.01191 0.41427 5.18518
30 4XMF HSM 0.005036 0.43112 5.92593
31 1ZB6 GST 0.007999 0.4086 5.92593
32 3PDT ADP 0.009761 0.40621 5.92593
33 1F52 ADP 0.01489 0.40137 5.92593
34 4QTB 38Z 0.0113 0.40064 5.92593
35 2OVD DAO 0.006156 0.43573 6.66667
36 5DMZ ADP 0.009171 0.40027 6.66667
37 3NZ1 3NY 0.01232 0.41841 7.40741
38 3TDV GDP 0.004601 0.41353 7.40741
39 1Y0G 8PP 0.01423 0.41042 7.40741
40 4YSX E23 0.02503 0.40223 7.40741
41 4W9N TCL 0.004426 0.44085 8.14815
42 3ZJX BOG 0.01678 0.41362 8.88889
43 2WQN ADP 0.01447 0.40196 8.88889
44 4DSU BZI 0.002037 0.46025 10.3704
45 5TVM PUT 0.01204 0.41811 10.5882
46 4TW7 37K 0.003705 0.41898 10.9375
47 5DG2 GAL GLC 0.005023 0.42239 11.1111
48 5F3I 5UJ 0.02659 0.40564 11.1111
49 1ZOY UQ1 0.001809 0.46272 11.8519
50 2AXR ABL 0.01303 0.4195 12.5926
51 1YFS ALA 0.01677 0.41418 12.5926
52 5KEW 6SB 0.02094 0.40665 13.8298
53 1Z03 OCH 0.01778 0.40988 14.0741
54 2D6M LBT 0.005552 0.43606 14.8148
55 5KR7 6X9 0.01584 0.40395 15.5556
56 4JR7 GNP 0.009148 0.40031 16.2963
57 5MRH Q9Z 0.007016 0.42574 17.7778
58 5EOB 5QQ 0.02787 0.40395 18.5185
59 2BMB PMM 0.009985 0.40962 19.2593
60 5D9G GLU ASN LEU TYR PHE GLN 0.01957 0.40347 25.1852
61 3WV6 GAL GLC 0.006478 0.42197 31.8519
62 3WV6 GAL BGC 0.009843 0.41584 31.8519
63 5XNA SHV 0.01148 0.41536 39.2593
64 3STK PLM 0.0001178 0.41097 48.4848
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