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Receptor
PDB id Resolution Class Description Source Keywords
5LJE 1.4 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF HOLO HUMAN CRBP1/K40L,Q108L MUTANT 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 = 250 nM
286.452 C20 H30 O CC1=C...
NA A:202;
Part of Protein;
none;
submit data
22.99 Na [Na+]
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 209 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 (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 : 5LJB; Ligand: RTL; Similar sites found with APoc: 142
This union binding pocket(no: 1) in the query (biounit: 5ljb.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 6FA4 D1W None
2 5LXB 7A9 None
3 3L5R 47X None
4 4RT1 C2E None
5 1SLT NDG GAL None
6 3Q8U ADP None
7 3ZXE PGZ None
8 5TPV TYD None
9 2E56 MYR None
10 4LRJ ANP None
11 4H6B 10X None
12 3RG9 WRA 0.740741
13 4LED XXR 1.48148
14 5I8T LAC 1.48148
15 1A78 TDG 1.49254
16 1OGX EQU 1.52672
17 5IXH OTP 2.22222
18 3VV1 GAL FUC 2.22222
19 1ZNY GDP 2.22222
20 6CAM BGC 2.22222
21 2P7Q GG6 2.25564
22 2YMZ LAT 2.30769
23 1OGZ EQU 2.4
24 3KYF 5GP 5GP 2.96296
25 3A76 SPD 2.96296
26 4FFG 0U8 2.96296
27 4BPZ GLC BGC BGC 2.96296
28 4MPO AMP 2.96296
29 2WA4 069 2.96296
30 2VDF OCT 3.7037
31 1ULE GLA GAL NAG 3.7037
32 1SDW IYT 3.7037
33 5ML3 DL3 3.7037
34 2YP9 SIA CMO 3.7037
35 1VA6 ADP 3.7037
36 1P0Z FLC 3.81679
37 4B1L FRU 4.44444
38 3RWP ABQ 4.44444
39 3RGA LSB 4.44444
40 3MTX PGT 4.44444
41 5GLT BGC GAL NAG GAL 4.44444
42 5LVP ATP 4.44444
43 2YKL NLD 4.44444
44 3KYG 5GP 5GP 4.44444
45 4B1M FRU FRU 4.44444
46 4RYV ZEA 4.44444
47 5FXD H7Y 4.44444
48 4WVW SLT 4.44444
49 2RDE C2E 4.44444
50 5LUN OGA 4.44444
51 3NRR D16 4.44444
52 5IXG OTP 4.44444
53 4IAW LIZ 5.18518
54 4NPL AKG 5.18518
55 3QRC SCR 5.18518
56 1NSZ GLC 5.18518
57 2AG4 OLA 5.18518
58 2AG4 LP3 5.18518
59 2AZ3 CDP 5.18518
60 3PPQ CHT 5.18518
61 4C2C ALA ALA ALA 5.18518
62 5H9Y BGC BGC BGC BGC 5.18518
63 2Z3U CRR 5.92593
64 4XMF HSM 5.92593
65 5EO8 TFU 5.92593
66 2X34 UQ8 5.92593
67 1W3T 3GR 5.92593
68 6FBZ MGP 5.92593
69 1ZB6 GST 5.92593
70 3PDT ADP 5.92593
71 2X32 OTP 5.92593
72 1IS3 LAT 5.92593
73 3MVH WFE 5.92593
74 3ZXR IQ1 5.92593
75 3ZXR P3S 5.92593
76 1F52 ADP 5.92593
77 1T66 FLU 5.92593
78 4QTB 38Z 5.92593
79 2OVD DAO 6.66667
80 5Y4R C2E 6.66667
81 2UWN SCR 6.66667
82 5A86 D7E 6.66667
83 3QPB URA 6.66667
84 3O7U O7U 6.66667
85 5NLD LBT 6.66667
86 5DMZ ADP 6.66667
87 4B2Z P5S 7.40741
88 3NZ1 3NY 7.40741
89 3TDV GDP 7.40741
90 1Y0G 8PP 7.40741
91 5HA0 LTD 7.40741
92 4YSX E23 7.40741
93 4W9N TCL 8.14815
94 3GM5 CIT 8.14815
95 3ORK AGS 8.14815
96 5DRB 5FJ 8.88889
97 3ZJX BOG 8.88889
98 5YJS SAL 8.88889
99 5DBX ANP 8.88889
100 2WQN ADP 8.88889
101 2XK9 XK9 8.88889
102 5EZU MYR 8.98876
103 2PVN P63 9.62963
104 5OCG 9R5 10.3704
105 2VVM PRO 10.3704
106 5TVM PUT 10.5882
107 4TW7 37K 10.9375
108 5DG2 GAL GLC 11.1111
109 5KWY C3S 11.1111
110 1ZOY UQ1 11.8519
111 1M5B BN1 11.8519
112 5EJL C2E 12.5926
113 2AXR ABL 12.5926
114 1YFS ALA 12.5926
115 3H0L ADP 12.766
116 1Y7P RIP 13.3333
117 5KEW 6SB 13.8298
118 3E8N ATP 14.0741
119 3E8N VRA 14.0741
120 1Z03 OCH 14.0741
121 2D6M LBT 14.8148
122 5NFB 8VT 14.8148
123 5KR7 6X9 15.5556
124 4JR7 GNP 16.2963
125 5MRH Q9Z 17.7778
126 3VSV XYP 17.7778
127 5EOB 5QQ 18.5185
128 2BMB PMM 19.2593
129 3E2M E2M 20
130 6FOF LAT 21.4815
131 2F2G HMH 21.4815
132 5KD6 LBU 22.2222
133 5B09 4MX 24.0385
134 5D9G GLU ASN LEU TYR PHE GLN 25.1852
135 3EW2 BTN 25.1852
136 3VQ2 LP4 LP5 MYR DAO 25.9259
137 5DEY 59T 28.8889
138 3NV3 GAL NAG MAN 31.1111
139 3WV6 GAL GLC 31.8519
140 3WV6 GAL BGC 31.8519
141 5XNA SHV 39.2593
142 3STK PLM 48.4848
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