Receptor
PDB id Resolution Class Description Source Keywords
4O9S 2.3 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF RETINOL-BINDING PROTEIN 4 (RBP4)IN COMP NON-RETINOID LIGAND HOMO SAPIENS RETINOL BINDING DISEASE MUTATION RETINOL-BINDING SECRETEDTRANSDUCTION TRANSPORT VISION VITAMIN A TRANSPORT PROTEPROTEIN BINDING
Ref.: STRUCTURE-ASSISTED DISCOVERY OF THE FIRST NON-RETIN LIGANDS FOR RETINOL-BINDING PROTEIN 4. BIOORG.MED.CHEM.LETT. V. 24 2885 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:211;
A:209;
A:207;
A:202;
A:205;
A:213;
A:204;
B:212;
B:213;
B:205;
B:203;
B:202;
B:214;
B:210;
B:208;
B:204;
B:206;
A:214;
B:207;
A:203;
B:209;
A:206;
A:208;
A:210;
A:212;
A:211;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
2RY B:201;
A:201;
Valid;
Valid;
none;
none;
ic50 = 0.28 uM
444.473 C22 H19 F3 N4 O S c1ccc...
PEG A:217;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
CL A:216;
A:215;
B:215;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4O9S 2.3 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF RETINOL-BINDING PROTEIN 4 (RBP4)IN COMP NON-RETINOID LIGAND HOMO SAPIENS RETINOL BINDING DISEASE MUTATION RETINOL-BINDING SECRETEDTRANSDUCTION TRANSPORT VISION VITAMIN A TRANSPORT PROTEPROTEIN BINDING
Ref.: STRUCTURE-ASSISTED DISCOVERY OF THE FIRST NON-RETIN LIGANDS FOR RETINOL-BINDING PROTEIN 4. BIOORG.MED.CHEM.LETT. V. 24 2885 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 4O9S ic50 = 0.28 uM 2RY C22 H19 F3 N4 O S c1ccc(c(c1....
2 4PSQ ic50 = 0.44 uM 2WL C21 H21 Cl N4 O c1ccc(cc1)....
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 4O9S ic50 = 0.28 uM 2RY C22 H19 F3 N4 O S c1ccc(c(c1....
2 4PSQ ic50 = 0.44 uM 2WL C21 H21 Cl N4 O c1ccc(cc1)....
3 1FEM - REA C20 H28 O2 CC1=C(C(CC....
4 1RBP Ki = 0.19 uM RTL C20 H30 O CC1=C(C(CC....
5 1KT5 - RTL C20 H30 O CC1=C(C(CC....
6 1ERB Kd = 8 nM ETR C22 H33 N O CCNC(=O)C=....
7 1BRP - RTL C20 H30 O CC1=C(C(CC....
8 1FEN - AZE C20 H30 CC=C(/C)C=....
9 1HBP - RTL C20 H30 O CC1=C(C(CC....
10 1FEL - FEN C26 H33 N O2 CC1=C(C(CC....
11 1KT6 - RTL C20 H30 O CC1=C(C(CC....
12 1AQB - RTL C20 H30 O CC1=C(C(CC....
13 1KT7 - RTL C20 H30 O CC1=C(C(CC....
14 1KT4 - RTL C20 H30 O CC1=C(C(CC....
15 1KT3 - RTL C20 H30 O CC1=C(C(CC....
16 1IIU - RTL C20 H30 O CC1=C(C(CC....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 141 families.
1 4O9S ic50 = 0.28 uM 2RY C22 H19 F3 N4 O S c1ccc(c(c1....
2 4PSQ ic50 = 0.44 uM 2WL C21 H21 Cl N4 O c1ccc(cc1)....
3 1FEM - REA C20 H28 O2 CC1=C(C(CC....
4 1RBP Ki = 0.19 uM RTL C20 H30 O CC1=C(C(CC....
5 1KT5 - RTL C20 H30 O CC1=C(C(CC....
6 1ERB Kd = 8 nM ETR C22 H33 N O CCNC(=O)C=....
7 1BRP - RTL C20 H30 O CC1=C(C(CC....
8 1FEN - AZE C20 H30 CC=C(/C)C=....
9 1HBP - RTL C20 H30 O CC1=C(C(CC....
10 1FEL - FEN C26 H33 N O2 CC1=C(C(CC....
11 1KT6 - RTL C20 H30 O CC1=C(C(CC....
12 1AQB - RTL C20 H30 O CC1=C(C(CC....
13 1KT7 - RTL C20 H30 O CC1=C(C(CC....
14 1KT4 - RTL C20 H30 O CC1=C(C(CC....
15 1KT3 - RTL C20 H30 O CC1=C(C(CC....
16 1IIU - RTL C20 H30 O CC1=C(C(CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2RY; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 2RY 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4O9S; Ligand: 2RY; Similar sites found: 90
This union binding pocket(no: 1) in the query (biounit: 4o9s.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2CBO TH2 0.01924 0.41945 None
2 1N5S ADL 0.0005515 0.40251 None
3 1KGI T4A 0.001769 0.40937 1.5748
4 2OVW CBI 0.004521 0.44881 2.32558
5 1ZB6 GST 0.0005804 0.44013 2.32558
6 1ZB6 DIN 0.0008852 0.43123 2.32558
7 3KYG 5GP 5GP 0.007546 0.41578 2.32558
8 4UWJ 7L5 0.01752 0.40744 2.32558
9 4UWJ MYA 0.01752 0.40744 2.32558
10 1M15 ADP 0.007392 0.40075 2.32558
11 1M15 ARG 0.007392 0.40075 2.32558
12 5HVJ ANP 0.03156 0.40576 2.7907
13 2ZV2 609 0.02146 0.40515 2.7907
14 4OYA 1VE 0.02059 0.4037 2.7907
15 3OV6 MK0 0.00513 0.40347 2.7907
16 4H2X G5A 0.01029 0.40278 2.7907
17 2W5F XYP XYP XYP 0.03597 0.40143 2.7907
18 4TWP AXI 0.01495 0.41052 2.95203
19 1DZK PRZ 0.002984 0.43448 3.18471
20 5A89 FMN 0.006209 0.41239 3.20513
21 5A89 ADP 0.006209 0.41239 3.20513
22 1IA9 ANP 0.009177 0.40499 3.25581
23 4Q3F TLA 0.02813 0.40799 3.4188
24 1QY1 PRZ 0.001504 0.40299 3.44828
25 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.003425 0.42403 3.53982
26 4KBA 1QM 0.0007006 0.48492 3.72093
27 2WSA 646 0.01155 0.42404 3.72093
28 2WSA MYA 0.01155 0.42404 3.72093
29 3T4L ZEA 0.0004186 0.40754 3.72093
30 4AU8 Z3R 0.0194 0.40734 3.72093
31 3ZJX BOG 0.03168 0.40668 3.72093
32 5W4W 9WG 0.005567 0.40203 3.72093
33 4MNS 2AX 0.01074 0.40673 3.77358
34 2I0D MUT 0.02252 0.40258 4.0404
35 4EZD SEY 0.01271 0.43823 4.18605
36 3QCQ 3Q0 0.006565 0.43577 4.18605
37 2GU8 796 0.008479 0.41514 4.18605
38 1OFL NGK GCD 0.002823 0.46155 4.65116
39 5BVE 4VG 0.003516 0.43557 4.65116
40 3DLG GWE 0.004184 0.43368 4.65116
41 2YKL NLD 0.00008755 0.41263 4.65116
42 1RYD GLC 0.02813 0.41203 4.65116
43 4X6F 3XU 0.003501 0.41977 4.7619
44 5AIG VPR 0.01733 0.40979 4.8
45 5L2J 6UL 0.003948 0.43617 5.10204
46 5L2J 70E 0.004232 0.43617 5.10204
47 2QLU ADE 0.005297 0.44131 5.11628
48 4BG4 ADP 0.002673 0.43266 5.11628
49 2XMY CDK 0.007911 0.42214 5.11628
50 3P7N FMN 0.004473 0.41888 5.11628
51 5J75 6GQ 0.0001738 0.414 5.11628
52 2G30 ALA ALA PHE 0.000001547 0.66345 5.42636
53 5EW9 5VC 0.007717 0.43878 5.5814
54 3PDT ADP 0.01513 0.40519 5.5814
55 5NBW 8SK 0.002647 0.44566 5.60748
56 2QHV OC9 0.0003168 0.50246 6.04651
57 5LIA 6XN 0.01694 0.40931 6.04651
58 3OQJ 3CX 0.01904 0.40775 6.04651
59 3LVW GSH 0.003927 0.41437 6.51163
60 3B6R ADP 0.001557 0.44757 6.97674
61 1O9U ADZ 0.01043 0.43628 6.97674
62 2YNE YNE 0.02698 0.40761 6.97674
63 2YNE NHW 0.02698 0.40761 6.97674
64 1N9L FMN 0.006402 0.41196 7.33945
65 3L5R 47X 0.03756 0.40096 7.37705
66 2XG5 EC5 0.003832 0.44616 7.90698
67 2XG5 EC2 0.003832 0.44616 7.90698
68 1OUK 084 0.03302 0.4092 7.90698
69 2RCU BUJ 0.01231 0.40809 7.90698
70 3TAY MN0 0.001506 0.42048 7.97546
71 2CM4 RCL 0.0006328 0.41704 8
72 3G08 FEE 0.002326 0.4395 8.08081
73 3L9R L9Q 0.002966 0.41698 8.16327
74 3L9R L9R 0.004368 0.41359 8.16327
75 3E8T UQ8 0.01876 0.40083 10.6977
76 5MRH Q9Z 0.01204 0.42196 11.1628
77 4NAE 1GP 0.01242 0.42862 11.6279
78 3I7V ATP 0.02218 0.41765 11.9403
79 2X4Z X4Z 0.001412 0.43015 14.8837
80 3SXF BK5 0.002535 0.41977 15.3488
81 3G5D 1N1 0.01413 0.40548 15.814
82 2GVJ DGB 0.001239 0.43969 17.2093
83 1WZ1 DNS 0.03454 0.40275 18.6992
84 4WHZ 3NL 0.01035 0.40658 20.4651
85 2GJ5 VD3 0.004882 0.41159 26.5432
86 4IAW LIZ 0.001902 0.45758 28.1915
87 2OVD DAO 0.03099 0.40603 28.5714
88 3FW4 CAQ 0.002454 0.40651 30.3371
89 2HZQ STR 0.000005152 0.41569 39.0805
90 5HA0 LTD 0.0008327 0.42905 41.6667
Pocket No.: 2; Query (leader) PDB : 4O9S; Ligand: 2RY; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 4o9s.bio3) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IGH 1EA 0.01312 0.41129 2.7907
2 4IGH FMN 0.01312 0.41129 2.7907
3 4IGH ORO 0.01312 0.41129 2.7907
4 5U98 1KX 0.01345 0.4069 5.05051
Pocket No.: 3; Query (leader) PDB : 4O9S; Ligand: 2RY; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4o9s.bio3) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4O9S; Ligand: 2RY; Similar sites found: 18
This union binding pocket(no: 4) in the query (biounit: 4o9s.bio2) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5L9V OGA 0.008266 0.42279 2.7907
2 5DRB 5FJ 0.01539 0.40242 2.7907
3 5DQ8 FLF 0.007691 0.40174 2.7907
4 4ITH RCM 0.00307 0.4004 3.25581
5 2AXR ABL 0.03034 0.4049 3.72093
6 4R38 RBF 0.001543 0.40689 4.28571
7 5IXG OTP 0.01815 0.40011 4.73373
8 3KRR DQX 0.01674 0.41193 5.11628
9 4P5Z Q7M 0.0101 0.40369 5.5814
10 2YAK OSV 0.007184 0.40167 6.51163
11 5HCY 60D 0.01562 0.40037 6.97674
12 1VJY 460 0.004704 0.41199 7.44186
13 1GT4 UNA 0.0004727 0.41088 7.54717
14 2XVD AS6 0.00526 0.40593 8.37209
15 5DEY 59T 0.0153 0.40741 8.83721
16 2RHQ GAX 0.004131 0.4072 9.76744
17 4JH6 FCN 0.01746 0.41078 10.8696
18 4CQE CQE 0.01138 0.40148 15.814
Feedback