Receptor
PDB id Resolution Class Description Source Keywords
2RCT 1.2 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF HUMAN HOLO CELLULAR RETINOL-BINDING PROTEIN II (CRBP-II) HOMO SAPIENS CELLULAR RETINOL-BINDING PROTEIN II CRBP II RETINOL LIPID-BINDING PROTEIN X-RAY STRUCTURE CYTOPLASM TRANSPORT VITAMIN A
Ref.: CRYSTAL STRUCTURE OF HUMAN CELLULAR RETINOL-BINDING PROTEIN II TO 1.2 A RESOLUTION. PROTEINS V. 70 1626 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
RTL A:140;
Valid;
none;
submit data
286.452 C20 H30 O CC1=C...
SO4 A:151;
A:152;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
TLA A:150;
Invalid;
none;
submit data
150.087 C4 H6 O6 [C@@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4QYN 1.19 Å NON-ENZYME: BINDING THE CRYSTAL STRUCTURES OF HOLO-WT HUMAN CELLULAR RETINOL BIN PROTEIN II (HCRBPII) BOUND TO RETINOL HOMO SAPIENS BETA BARREL TRANSFER PROTEIN KIDNEY LOVER TRANSPORT PROT
Ref.: STRUCTURES OF HOLO WILD-TYPE HUMAN CELLULAR RETINOL PROTEIN II (HCRBPII) BOUND TO RETINOL AND RETINAL. ACTA CRYSTALLOGR.,SECT.D V. 70 3226 2014
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 4QZU Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
2 4QYN Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
3 2RCT - RTL C20 H30 O CC1=C(C(CC....
4 4QZT Kd = 2 nM RTL C20 H30 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: 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 : 4QYN; Ligand: RTL; Similar sites found: 73
This union binding pocket(no: 1) in the query (biounit: 4qyn.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IAW LIZ 0.001146 0.46324 None
2 2OVD DAO 0.002479 0.46033 None
3 3RGA LSB 0.0006657 0.45925 None
4 2VQ5 HBA 0.00348 0.45536 None
5 3VV1 GAL FUC 0.006985 0.43209 None
6 3Q8U ADP 0.01444 0.4188 None
7 1SN0 T44 0.007946 0.4178 None
8 1KGI T4A 0.00231 0.41049 None
9 1OGZ EQU 0.01428 0.40556 None
10 1N5S ADL 0.01042 0.40467 None
11 2BOS GLA GAL 0.0145 0.40355 None
12 2HZQ STR 0.0164 0.41722 1.50376
13 3CBC DBS 0.02297 0.40331 1.50376
14 3FW4 CAQ 0.002603 0.40307 1.50376
15 1P0Z FLC 0.01755 0.41752 1.52672
16 4QPW XYP XYP XYP 0.003714 0.44499 2.25564
17 3ZJX BOG 0.0098 0.4298 2.25564
18 4NPL AKG 0.01213 0.42426 2.25564
19 2AZ3 CDP 0.02252 0.40782 2.25564
20 5TPV TYD 0.01569 0.41762 3.00752
21 3KYF 5GP 5GP 0.01327 0.41106 3.00752
22 1ZNY GDP 0.01912 0.41153 3.7594
23 4XMF HSM 0.001998 0.45143 4.51128
24 3M3E GAL A2G NPO 0.0129 0.42422 4.51128
25 3WIR BGC 0.02409 0.40733 4.51128
26 3KYG 5GP 5GP 0.009131 0.40729 4.51128
27 5F6U 5VK 0.01514 0.40632 4.51128
28 4XCB AKG 0.02491 0.40554 4.51128
29 5V3D FCN 0.02774 0.40319 4.51128
30 4K55 H6P 0.008402 0.44538 4.83871
31 5L6G XYP 0.01019 0.43339 5.26316
32 1F52 ADP 0.01704 0.40187 5.26316
33 3QRC SCR 0.00123 0.46397 6.01504
34 2YKL NLD 0.005853 0.42416 6.01504
35 1QKQ MAN 0.007295 0.41762 6.01504
36 1I7M PUT 0.01592 0.40898 6.01504
37 5KEW 6SB 0.02529 0.40759 6.01504
38 5X7Q GLC GLC GLC GLC GLC 0.02371 0.41217 6.76692
39 4OCT AKG 0.01631 0.40664 6.76692
40 4ZJS 4P0 0.02753 0.40686 7.5188
41 4FFG LBS 0.01918 0.40514 7.5188
42 1YKD CMP 0.009962 0.40209 7.5188
43 1I06 TZL 0.03027 0.40112 7.5188
44 5MRH Q9Z 0.01095 0.41948 8.27068
45 4NG2 OHN 0.004509 0.41042 8.84956
46 4WOE ADP 0.02512 0.40874 9.02256
47 5TVM PUT 0.007564 0.43338 9.41177
48 4B1M FRU FRU 0.00263 0.45639 9.77444
49 3MTX PGT 0.001096 0.44209 9.77444
50 4HPP GLU 0.006056 0.43799 9.77444
51 4B1L FRU 0.01906 0.41203 9.77444
52 2P7Q GG6 0.0176 0.40906 9.77444
53 1I82 BGC BGC 0.03527 0.40054 9.77444
54 2VFT SOR 0.002984 0.44289 10.5263
55 1JL0 PUT 0.0161 0.40412 10.5263
56 2VDF OCT 0.002372 0.4556 11.2782
57 1OIJ AKG 0.02934 0.40358 11.2782
58 2GTF P1R 0.002913 0.42862 12.0301
59 5KJW 53C 0.02273 0.41262 12.0301
60 4DSU BZI 0.01398 0.41874 12.782
61 5H9Y BGC BGC BGC BGC 0.007552 0.41485 14.2857
62 5KR7 6X9 0.01411 0.40581 14.2857
63 3GM5 CIT 0.02861 0.40358 15.7895
64 4QXB OGA 0.02569 0.40073 15.7895
65 1UNB AKG 0.0007383 0.40947 16.5414
66 1UNB PN1 0.0006012 0.40389 16.5414
67 4YSX E23 0.02814 0.40278 16.5414
68 4IGQ THR M3L GLN 0.008321 0.40221 16.5414
69 3HPY MCT 0.02081 0.40962 20.3008
70 3DZ6 PUT 0.02356 0.40231 20.8955
71 5DMZ ADP 0.003381 0.41935 22.5564
72 5XNA SHV 0.0008832 0.48431 42.8571
73 1LFO OLA 0.005478 0.41017 48.4375
Pocket No.: 2; Query (leader) PDB : 4QYN; Ligand: RTL; Similar sites found: 21
This union binding pocket(no: 2) in the query (biounit: 4qyn.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1RYD GLC 0.02563 0.40378 2.25564
2 4BPZ GLC BGC BGC 0.0147 0.40792 3.00752
3 4YVN EBS 0.00795 0.42842 3.7594
4 5I8T LAC 0.01859 0.40714 3.7594
5 4L4J NAG NAG BMA MAN NAG 0.003913 0.43357 6.01504
6 3HAV ATP 0.01546 0.41437 6.01504
7 4H6B 10Y 0.01698 0.40072 6.01504
8 5LXB 7A9 0.01078 0.42191 7.5188
9 1Z03 OCH 0.01178 0.41727 7.5188
10 2JIG PD2 0.01405 0.40889 7.5188
11 1ZOY UQ1 0.001122 0.47249 8.27068
12 4EE7 PIS 0.003266 0.45147 8.27068
13 4J25 OGA 0.007215 0.42327 8.27068
14 5FPE 3TR 0.01977 0.41008 8.27068
15 3NZ1 3NY 0.01923 0.40557 8.27068
16 2GQS C2R 0.01066 0.40262 8.27068
17 4A91 GLU 0.007226 0.41608 11.2782
18 4NS0 PIO 0.0326 0.40368 11.2782
19 1Y7P RIP 0.01551 0.41763 12.782
20 2MPR BGC GLC GLC 0.01386 0.41367 16.5414
21 2VVM PRO 0.02557 0.40405 29.3233
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