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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 510 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 (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 175 families.
1 1OPB Kd = 50 nM RET C20 H28 O CC1=C(C(CC....
2 5LJG - PLM C16 H32 O2 CCCCCCCCCC....
3 5LJC Kd = 65 nM RTL C20 H30 O CC1=C(C(CC....
4 5HBS Kd = 18.5 nM RTL C20 H30 O CC1=C(C(CC....
5 5H8T Kd = 18.5 nM RTL C20 H30 O CC1=C(C(CC....
6 5LJE Kd = 250 nM RTL C20 H30 O CC1=C(C(CC....
7 5LJD Kd = 70 nM RTL C20 H30 O CC1=C(C(CC....
8 5LJB Kd = 4.5 nM RTL C20 H30 O CC1=C(C(CC....
9 1CRB - RTL C20 H30 O CC1=C(C(CC....
10 5HA1 Kd = 64.1 nM RNE C20 H31 N CC1=C(C(CC....
11 4QYN Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
12 2RCT - RTL C20 H30 O CC1=C(C(CC....
13 4QZT Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
14 1KQW - RTL C20 H30 O CC1=C(C(CC....
50% Homology Family (113)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 298 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 5L8O - CHD C24 H40 O5 C[C@H](CCC....
22 5L8N Kd = 31 uM 6RQ C9 H11 N3 Cc1cc2c(cc....
23 3WBG - 2AN C16 H13 N O3 S c1ccc(cc1)....
24 5HZ5 Ki = 0.086 uM 65X C21 H19 Cl N6 c1ccc(cc1)....
25 5UR9 Ki = 0.9 uM 8KS C28 H22 O4 c1ccc(cc1)....
26 1B56 - PLM C16 H32 O2 CCCCCCCCCC....
27 5D4A - 57Q C17 H15 N O2 c1ccc(cc1)....
28 5Y0F Ki = 0.21 uM 8JO C18 H14 F N O5 S COc1ccc(c2....
29 5D47 Ki = 0.1 uM L19 C26 H24 N2 O3 COc1cnccc1....
30 5Y12 Ki = 0.59 uM 8JX C16 H19 N O5 S COc1ccc(c2....
31 5D48 Ki = 0.03 uM L96 C28 H31 N3 O3 Cc1c(c(n[n....
32 5D45 Ki = 0.12 uM 57P C26 H23 N O2 c1ccc(cc1)....
33 5Y0X Ki = 7.75 uM 8JR C18 H14 F N O5 S COc1ccc(c2....
34 5Y0G Ki = 0.2 uM 8JL C18 H14 F N O5 S COc1ccc(c2....
35 5Y13 Ki = 1.16 uM 8K0 C15 H16 Br N O4 S c1ccc2c(c1....
36 5URA Ki = 0.4 uM 8KS C28 H22 O4 c1ccc(cc1)....
37 1FDQ Kd = 53.4 nM HXA C22 H32 O2 CCC=C/CC=C....
38 2G78 - REA C20 H28 O2 CC1=C(C(CC....
39 2CBS Ki = 6 nM R13 C23 H30 O2 CC(=C/C(=O....
40 1CBS - REA C20 H28 O2 CC1=C(C(CC....
41 2FR3 Kd = 2 nM REA C20 H28 O2 CC1=C(C(CC....
42 3CWK Kd = 250 nM REA C20 H28 O2 CC1=C(C(CC....
43 3CBS Ki = 58 nM R12 C20 H24 O3 Cc1cc(c(c(....
44 2G79 Kd = 120 nM RET C20 H28 O CC1=C(C(CC....
45 2G7B - AZE C20 H30 CC=C(/C)C=....
46 1CBQ - RE9 C20 H28 O2 CC(=C/C(=O....
47 4TKB - DAO C12 H24 O2 CCCCCCCCCC....
48 4TJZ - DKA C10 H20 O2 CCCCCCCCCC....
49 1HMT Kd = 1.64 uM STE C18 H36 O2 CCCCCCCCCC....
50 4TKJ - PLM C16 H32 O2 CCCCCCCCCC....
51 5HZ9 Ki = 0.093 uM 5M8 C17 H12 Cl N O2 Cc1c(c(c2c....
52 4WBK - STE C18 H36 O2 CCCCCCCCCC....
53 3WVM - STE C18 H36 O2 CCCCCCCCCC....
54 4TKH - MYR C14 H28 O2 CCCCCCCCCC....
55 1HMR Kd = 0.28 uM ELA C18 H34 O2 CCCCCCCCC=....
56 1HMS Kd = 0.43 uM OLA C18 H34 O2 CCCCCCCCC=....
57 2HMB - PLM C16 H32 O2 CCCCCCCCCC....
58 3VG3 - PLM C16 H32 O2 CCCCCCCCCC....
59 3B2H - PLM C16 H32 O2 CCCCCCCCCC....
60 3B2K - PLM C16 H32 O2 CCCCCCCCCC....
61 3VG6 - PLM C16 H32 O2 CCCCCCCCCC....
62 3VG5 - PLM C16 H32 O2 CCCCCCCCCC....
63 3VG7 - PLM C16 H32 O2 CCCCCCCCCC....
64 3STM - PLM C16 H32 O2 CCCCCCCCCC....
65 3VG2 - PLM C16 H32 O2 CCCCCCCCCC....
66 3B2I - PLM C16 H32 O2 CCCCCCCCCC....
67 3B2L - PLM C16 H32 O2 CCCCCCCCCC....
68 3B2J - PLM C16 H32 O2 CCCCCCCCCC....
69 3VG4 - PLM C16 H32 O2 CCCCCCCCCC....
70 1OPB Kd = 50 nM RET C20 H28 O CC1=C(C(CC....
71 2Q9S - EIC C18 H32 O2 CCCCCC=C/C....
72 2QM9 Kd = 17 nM TDZ C24 H27 N O5 S Cc1c(c2c(c....
73 2QO4 - CHD C24 H40 O5 C[C@H](CCC....
74 2QO6 - CHD C24 H40 O5 C[C@H](CCC....
75 2QO5 - CHD C24 H40 O5 C[C@H](CCC....
76 1TW4 - CHD C24 H40 O5 C[C@H](CCC....
77 5BVT - PAM C16 H30 O2 CCCCCCC=C/....
78 3ELZ - CHD C24 H40 O5 C[C@H](CCC....
79 3EM0 - CHD C24 H40 O5 C[C@H](CCC....
80 4AZQ - G2A C23 H46 O4 CCCCCCCCCC....
81 4AZP Ki = 1.26 uM A9M C22 H45 N O2 CCCCCCCCCC....
82 5LJG - PLM C16 H32 O2 CCCCCCCCCC....
83 5LJC Kd = 65 nM RTL C20 H30 O CC1=C(C(CC....
84 5HBS Kd = 18.5 nM RTL C20 H30 O CC1=C(C(CC....
85 5H8T Kd = 18.5 nM RTL C20 H30 O CC1=C(C(CC....
86 5LJE Kd = 250 nM RTL C20 H30 O CC1=C(C(CC....
87 5LJD Kd = 70 nM RTL C20 H30 O CC1=C(C(CC....
88 5LJB Kd = 4.5 nM RTL C20 H30 O CC1=C(C(CC....
89 1CRB - RTL C20 H30 O CC1=C(C(CC....
90 5HA1 Kd = 64.1 nM RNE C20 H31 N CC1=C(C(CC....
91 4QZU Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
92 4QYN Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
93 2RCT - RTL C20 H30 O CC1=C(C(CC....
94 4QZT Kd = 2 nM RTL C20 H30 O CC1=C(C(CC....
95 1VYF Kd = 9 nM OLA C18 H34 O2 CCCCCCCCC=....
96 1VYG Kd = 10 nM ACD C20 H32 O2 CCCCCC=C/C....
97 2FT9 - CHD C24 H40 O5 C[C@H](CCC....
98 2FTB - OLA C18 H34 O2 CCCCCCCCC=....
99 1ICM - MYR C14 H28 O2 CCCCCCCCCC....
100 1ICN - OLA C18 H34 O2 CCCCCCCCC=....
101 2IFB Ki = 3.6 uM PLM C16 H32 O2 CCCCCCCCCC....
102 5BVS - EIC C18 H32 O2 CCCCCC=C/C....
103 6EW4 - PLM C16 H32 O2 CCCCCCCCCC....
104 2WUT - PLM C16 H32 O2 CCCCCCCCCC....
105 4BVM - PLM C16 H32 O2 CCCCCCCCCC....
106 6EW2 - PLM C16 H32 O2 CCCCCCCCCC....
107 4D6B - PLM C16 H32 O2 CCCCCCCCCC....
108 6EW5 - PLM C16 H32 O2 CCCCCCCCCC....
109 5N4Q - PLM C16 H32 O2 CCCCCCCCCC....
110 4D6A - PLM C16 H32 O2 CCCCCCCCCC....
111 5N4P - PLM C16 H32 O2 CCCCCCCCCC....
112 5N4M - PLM C16 H32 O2 CCCCCCCCCC....
113 1KQW - RTL C20 H30 O CC1=C(C(CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RTL; Similar ligands found: 11
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 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 with APoc: 122
This union binding pocket(no: 1) in the query (biounit: 4qyn.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 6GNO XDI None
2 4IAW LIZ None
3 2OVD DAO None
4 2VQ5 HBA None
5 3VV1 GAL FUC None
6 3Q8U ADP None
7 5LHT TIH None
8 3RGA LSB None
9 1KGI T4A None
10 1N5S ADL None
11 2BOS GLA GAL None
12 2HZQ STR 1.50376
13 3FW4 CAQ 1.50376
14 3CBC DBS 1.50376
15 1P0Z FLC 1.52672
16 4QPW XYP XYP XYP 2.25564
17 3ZJX BOG 2.25564
18 4NPL AKG 2.25564
19 2AZ3 CDP 2.25564
20 3L5R 47X 2.45902
21 5TPV TYD 3.00752
22 3KYF 5GP 5GP 3.00752
23 1ZNY GDP 3.7594
24 6D61 4AA 3.7594
25 5B09 4MX 3.84615
26 4XMF HSM 4.51128
27 3M3E GAL A2G NPO 4.51128
28 1ZS6 ADP 4.51128
29 3KJQ B94 4.51128
30 3E8T UQ8 4.51128
31 5ML3 DL3 4.51128
32 3KYG 5GP 5GP 4.51128
33 5F6U 5VK 4.51128
34 4XCB AKG 4.51128
35 2JLD AG1 4.51128
36 3WIR BGC 4.51128
37 5V3D FCN 4.51128
38 4UWJ 7L5 4.51128
39 4UWJ MYA 4.51128
40 4K55 H6P 4.83871
41 2AG4 LP3 5.26316
42 2AG4 OLA 5.26316
43 2XMY CDK 5.26316
44 5L6G XYP 5.26316
45 5Z9S BGC 5.26316
46 1F52 ADP 5.26316
47 2Z3U CRR 6.01504
48 5EO8 TFU 6.01504
49 3QRC SCR 6.01504
50 2A1L PCW 6.01504
51 6MPT C30 6.01504
52 2ART LPA AMP 6.01504
53 2YKL NLD 6.01504
54 1I7M PUT 6.01504
55 5KEW 6SB 6.01504
56 3ZXR P3S 6.01504
57 3ZXR IQ1 6.01504
58 1QKQ MAN 6.01504
59 3E9I XAH 6.01504
60 6BU0 IHP 6.10687
61 5F7U GLC GLC 6.76692
62 2YP9 SIA CMO 6.76692
63 5X7Q GLC GLC GLC GLC GLC 6.76692
64 4OCT AKG 6.76692
65 4CS4 ANP 6.76692
66 4XIZ LPP 7.14286
67 5LXB 7A9 7.5188
68 1ERB ETR 7.5188
69 4ZJS 4P0 7.5188
70 4FFG LBS 7.5188
71 1YKD CMP 7.5188
72 1I06 TZL 7.5188
73 5EZU MYR 7.86517
74 3A7R LAQ 8.27068
75 5MRH Q9Z 8.27068
76 2YNE NHW 8.27068
77 2YNE YNE 8.27068
78 3A5Z KAA 8.27068
79 4RYV ZEA 8.27068
80 4NG2 OHN 8.84956
81 3I7S PYR 9.02256
82 4WOE ADP 9.02256
83 3O7U O7U 9.02256
84 1ODM ASV 9.02256
85 5TVM PUT 9.41177
86 2GJ5 VD3 9.77444
87 4B1M FRU FRU 9.77444
88 3MTX PGT 9.77444
89 4HPP GLU 9.77444
90 4B1L FRU 9.77444
91 2VCN ISZ 9.77444
92 2P7Q GG6 9.77444
93 1I82 BGC BGC 9.77444
94 4RF7 ARG 10.5263
95 2VFT SOR 10.5263
96 2VDF OCT 11.2782
97 1OIJ AKG 11.2782
98 6DW2 HD4 12.0301
99 2GTF P1R 12.0301
100 2Z77 HE7 12.0301
101 5KJW 53C 12.0301
102 1Y7P RIP 12.782
103 3E85 BSU 12.782
104 2E5A LAQ 14.2857
105 5H9Y BGC BGC BGC BGC 14.2857
106 5KR7 6X9 14.2857
107 4MNS 2AX 15.0376
108 5L2R MLA 15.7895
109 3GM5 CIT 15.7895
110 4QXB OGA 15.7895
111 1UNB PN1 16.5414
112 1UNB AKG 16.5414
113 4YSX E23 16.5414
114 2AGC DAO 16.5414
115 4IGQ THR M3L GLN 16.5414
116 3RUG DB6 18.1818
117 3HPY MCT 20.3008
118 3DZ6 PUT 20.8955
119 5DMZ ADP 22.5564
120 1F5F DHT 31.5789
121 5XNA SHV 42.8571
122 1LFO OLA 48.4375
Pocket No.: 2; Query (leader) PDB : 4QYN; Ligand: RTL; Similar sites found with APoc: 59
This union binding pocket(no: 2) in the query (biounit: 4qyn.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5DRB 5FJ None
2 6FA4 D1W None
3 3E2M E2M 2.25564
4 1VA6 ADP 2.25564
5 1VA6 P2S 2.25564
6 1RYD GLC 2.25564
7 4TW7 37K 2.34375
8 5K21 6QF 3.00752
9 4BPZ GLC BGC BGC 3.00752
10 5UIU 8CG 3.00752
11 4YVN EBS 3.7594
12 5I8T LAC 3.7594
13 3LVW GSH 4.51128
14 5VAD PRO 4.51128
15 2RDE C2E 4.51128
16 5O9W AKG 5.26316
17 5OX6 A1Z 5.26316
18 6FBZ MGP 5.26316
19 2BPM 529 5.26316
20 4I54 1C1 5.26316
21 4L4J NAG NAG BMA MAN NAG 6.01504
22 1SDW IYT 6.01504
23 3E8N VRA 6.01504
24 3E8N ATP 6.01504
25 3HAV ATP 6.01504
26 4K5S PM0 6.01504
27 6CGD GNP 6.01504
28 5KWY C3S 6.01504
29 4H6B 10Y 6.01504
30 4CS4 AXZ 6.76692
31 5F3I 5UJ 6.76692
32 1NNU NAD 6.76692
33 1NNU TCT 6.76692
34 1W3T 3GR 7.5188
35 1Z03 OCH 7.5188
36 2JIG PD2 7.5188
37 4P8K 38C 7.5188
38 4P8K FAD 7.5188
39 3DLG GWE 7.5188
40 1ZOY UQ1 8.27068
41 4EE7 PIS 8.27068
42 4J25 OGA 8.27068
43 5FPE 3TR 8.27068
44 3NZ1 3NY 8.27068
45 2GQS C2R 8.27068
46 6C0T EE4 9.02256
47 5HA0 LTD 9.02256
48 2WSA 646 9.77444
49 2WSA MYA 9.77444
50 5DQ8 FLF 9.77444
51 4A91 GLU 11.2782
52 5IXH OTP 11.2782
53 4NS0 PIO 11.2782
54 4WW7 AMP 12.782
55 3PE2 E1B 14.2857
56 5U98 1KX 15.0376
57 2MPR BGC GLC GLC 16.5414
58 2VVM PRO 29.3233
59 1KDK DHT 31.5789
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