Receptor
PDB id Resolution Class Description Source Keywords
2YG2 1.7 Å NON-ENZYME: OTHER STRUCTURE OF APOLIOPROTEIN M IN COMPLEX WITH SPHINGOSINE 1-P HOMO SAPIENS LIPID TRANSPORT LIPOCALIN HDL
Ref.: ENDOTHELIUM-PROTECTIVE SPHINGOSINE-1-PHOSPHATE PROV HDL-ASSOCIATED APOLIPOPROTEIN M. PROC.NATL.ACAD.SCI.USA V. 108 9613 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FLC A:401;
Valid;
none;
submit data
189.1 C6 H5 O7 C(C(=...
S1P A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
379.472 C18 H38 N O5 P CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YG2 1.7 Å NON-ENZYME: OTHER STRUCTURE OF APOLIOPROTEIN M IN COMPLEX WITH SPHINGOSINE 1-P HOMO SAPIENS LIPID TRANSPORT LIPOCALIN HDL
Ref.: ENDOTHELIUM-PROTECTIVE SPHINGOSINE-1-PHOSPHATE PROV HDL-ASSOCIATED APOLIPOPROTEIN M. PROC.NATL.ACAD.SCI.USA V. 108 9613 2011
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 2WEW - MYR C14 H28 O2 CCCCCCCCCC....
2 2WEX - GYM C17 H34 O4 CCCCCCCCCC....
3 2YG2 - S1P C18 H38 N O5 P CCCCCCCCCC....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 2WEW - MYR C14 H28 O2 CCCCCCCCCC....
2 2WEX - GYM C17 H34 O4 CCCCCCCCCC....
3 2YG2 - S1P C18 H38 N O5 P CCCCCCCCCC....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 2WEW - MYR C14 H28 O2 CCCCCCCCCC....
2 2WEX - GYM C17 H34 O4 CCCCCCCCCC....
3 2YG2 - S1P C18 H38 N O5 P CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FLC; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 FLC 1 1
2 FE CIT 0.95 0.875
Ligand no: 2; Ligand: S1P; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 S1P 1 1
2 SPU 0.65625 0.775862
3 SPH 0.584906 0.666667
4 SQS 0.584906 0.666667
5 1PW 0.553846 0.865385
6 1PZ 0.529412 0.849057
7 1PX 0.529412 0.849057
8 NKP 0.442857 0.711538
9 2ED 0.421875 0.622642
10 18C 0.41791 0.611111
11 16C 0.41791 0.611111
12 SPL 0.41791 0.611111
13 6CM 0.411765 0.611111
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YG2; Ligand: FLC; Similar sites found: 100
This union binding pocket(no: 1) in the query (biounit: 2yg2.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WVW SLT 0.0002841 0.50843 None
2 5T7I LAT NAG GAL 0.003183 0.45871 None
3 4Z28 BTN 0.00403 0.44137 None
4 1SN0 T44 0.003703 0.43859 None
5 2IFB PLM 0.0006497 0.41926 None
6 2PR5 FMN 0.008601 0.40624 None
7 2YMZ LAT 0.005537 0.40521 None
8 5JSP DQY 0.003906 0.45541 1.74419
9 1Y9Q MED 0.03232 0.40673 1.74419
10 3AJH BL3 0.01302 0.40476 1.74419
11 2ZHL NAG GAL GAL NAG 0.009022 0.4198 2.02703
12 1QFT HSM 0.003898 0.4291 2.32558
13 2AGC DAO 0.01564 0.41614 2.46914
14 2Z77 NCA 0.0231 0.41162 2.8777
15 4OPC FDA 0.01738 0.42188 2.90698
16 4OPC PGT 0.02 0.42186 2.90698
17 1Y0G 8PP 0.005271 0.41539 2.90698
18 4XBT FLC 0.006323 0.41568 3.22581
19 4XBT 3ZQ 0.008231 0.41048 3.22581
20 1GUI BGC BGC BGC BGC BGC BGC 0.03138 0.40458 3.22581
21 4Y24 TD2 0.002935 0.44821 3.24675
22 4ZU4 4TG 0.002691 0.43656 3.37838
23 2E56 MYR 0.000743 0.43732 3.47222
24 4P7X YCP 0.001321 0.44655 3.48837
25 4OCT AKG 0.005405 0.43503 3.48837
26 1VJ7 GDP 0.01127 0.42802 3.48837
27 4XDA RIB 0.01584 0.41175 3.48837
28 4BG4 ADP 0.008827 0.4091 3.48837
29 1GP6 DH2 0.003225 0.40871 3.48837
30 1GP6 QUE 0.003725 0.40332 3.48837
31 1GP6 SIN 0.003225 0.40167 3.48837
32 5ML3 DL3 0.0009001 0.44196 4.02685
33 1WUB OTP 0.003023 0.42556 4.06977
34 5FS0 5JC 0.01409 0.41846 4.06977
35 2OVW CBI 0.02647 0.4044 4.06977
36 3P7N FMN 0.01018 0.40299 4.06977
37 4CB5 93G 0.01768 0.40555 4.19162
38 3I7V ATP 0.01113 0.42835 4.47761
39 1Z03 OCH 0.01914 0.41593 4.65116
40 4RLT FSE 0.01437 0.40995 4.7619
41 5AIG VPR 0.02001 0.40667 4.8
42 1W6P NDG GAL 0.005434 0.42865 5.22388
43 1W6O LAT 0.01536 0.40755 5.22388
44 1GZW GAL BGC 0.01537 0.40595 5.22388
45 4YGF AZM 0.004166 0.42025 5.23256
46 1T27 PCW 0.004063 0.42015 5.23256
47 1DZT ATY 0.0224 0.41135 5.23256
48 5LY2 OGA 0.03656 0.40076 5.23256
49 4QJP V1F 0.005233 0.40024 5.23256
50 4BJ8 BTN 0.01641 0.40008 5.55556
51 3SAO NKN 0.0000354 0.42318 5.625
52 3VQ2 LP4 LP5 MYR DAO 0.0007977 0.4499 5.81395
53 4H6B 10Y 0.01242 0.42127 5.81395
54 2WA4 069 0.01009 0.41744 6.39535
55 3FW4 CAQ 0.002773 0.40509 6.39535
56 3W9K MYR 0.01815 0.40141 6.47482
57 4JH6 FCN 0.01694 0.41436 6.52174
58 2ET1 GLV 0.002687 0.46395 6.97674
59 2AXR ABL 0.007185 0.44091 6.97674
60 3ZGJ RMN 0.01994 0.41499 6.97674
61 2GC0 PAN 0.009509 0.40762 6.97674
62 4AMF ACP 0.02972 0.4039 6.97674
63 2Y7P SAL 0.03694 0.40082 6.97674
64 5L6G XYP 0.0007509 0.4937 7.55814
65 3WV6 GAL GLC 0.0005154 0.46507 7.55814
66 3WV6 GAL BGC 0.003921 0.42921 7.55814
67 1ZB6 DIN 0.004762 0.40203 7.55814
68 3A6T 8OG 0.01494 0.40197 7.75194
69 4Q5H ANP 0.01377 0.40029 7.89474
70 4XCB AKG 0.0157 0.42046 8.13953
71 1QY1 PRZ 0.0001166 0.47963 8.72093
72 4COQ SAN 0.003706 0.46047 8.72093
73 1I06 TZL 0.006693 0.4399 8.72093
74 1EPB REA 0.0000002582 0.62261 9.14634
75 4WOE ADP 0.002526 0.46364 9.30233
76 1NVM OXL 0.01114 0.41939 9.30233
77 2XMY CDK 0.02466 0.4002 9.30233
78 1ULE GLA GAL NAG 0.0001887 0.52406 9.33333
79 4JNJ BTN 0.01373 0.40719 9.56522
80 5CJF 520 0.001665 0.45543 9.88372
81 4FFG 0U8 0.02152 0.41325 9.88372
82 5C5T AKG 0.01827 0.41268 9.88372
83 4GYI ADP 0.02167 0.40123 9.88372
84 1ODM ASV 0.0005092 0.43342 10.4651
85 1LNM DTX 0.005715 0.41078 11.0465
86 1I7E IBS 0.0244 0.41528 11.6279
87 3FW3 ETS 0.01476 0.41328 11.6279
88 1OI6 TMP 0.02117 0.4161 12.7907
89 1C1L GAL BGC 0.01076 0.42239 13.1387
90 5C3R HMU 0.001049 0.45108 13.9535
91 5C3R AKG 0.001049 0.45108 13.9535
92 3RGA LSB 0.00268 0.43665 14.5349
93 4X5S AZM 0.002231 0.47167 15.1163
94 2BO9 VAL 0.005152 0.44585 15.6977
95 3LVW GSH 0.006229 0.4061 15.6977
96 5H9Q TD2 0.0001012 0.52733 16.129
97 2E27 AB0 0.007328 0.42419 16.8067
98 5NCF 8T5 0.001807 0.46963 20.354
99 1DZK PRZ 0.002225 0.4404 24.8408
100 2GJ5 VD3 0.0001505 0.40988 32.0988
Pocket No.: 2; Query (leader) PDB : 2YG2; Ligand: S1P; Similar sites found: 100
This union binding pocket(no: 2) in the query (biounit: 2yg2.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WVW SLT 0.0002269 0.50843 None
2 5T7I LAT NAG GAL 0.002567 0.45871 None
3 2IFB PLM 0.0003588 0.44916 None
4 2PR5 FMN 0.006734 0.40624 None
5 2YMZ LAT 0.004641 0.40521 None
6 5JSP DQY 0.002825 0.45787 1.74419
7 1Y9Q MED 0.02706 0.40673 1.74419
8 2ZHL NAG GAL GAL NAG 0.01209 0.40904 2.02703
9 1QFT HSM 0.003046 0.4291 2.32558
10 2AGC DAO 0.002634 0.45063 2.46914
11 4OPC FDA 0.01224 0.43677 2.90698
12 4OPC PGT 0.0304 0.4201 2.90698
13 1Y0G 8PP 0.01039 0.41087 2.90698
14 3RE4 TO1 0.009805 0.40587 2.90698
15 3NW7 LGV 0.0148 0.4058 2.90698
16 4XBT FLC 0.005816 0.41256 3.22581
17 4XBT 3ZQ 0.006473 0.41048 3.22581
18 1GUI BGC BGC BGC BGC BGC BGC 0.02599 0.40458 3.22581
19 4Y24 TD2 0.002323 0.44821 3.24675
20 4ZU4 4TG 0.002358 0.43418 3.37838
21 2E56 MYR 0.001395 0.43622 3.47222
22 4P7X YCP 0.002333 0.43029 3.48837
23 4OCT AKG 0.00614 0.42751 3.48837
24 4XDA RIB 0.01285 0.41175 3.48837
25 4BG4 ADP 0.007111 0.40865 3.48837
26 4QCK ASD 0.0006281 0.40833 3.48837
27 3TL1 JRO 0.02677 0.40391 3.77358
28 5ML3 DL3 0.0009423 0.45145 4.02685
29 4N14 WR7 0.001899 0.46091 4.06977
30 1WUB OTP 0.01123 0.40937 4.06977
31 3P7N FMN 0.007989 0.40299 4.06977
32 2OVW CBI 0.02405 0.40218 4.06977
33 4CB5 93G 0.0153 0.40412 4.19162
34 3I7V ATP 0.01235 0.42119 4.47761
35 1Z03 OCH 0.01482 0.41728 4.65116
36 5AIG VPR 0.01229 0.4127 4.8
37 1W6P NDG GAL 0.004554 0.42865 5.22388
38 1W6O LAT 0.01295 0.40755 5.22388
39 1GZW GAL BGC 0.01296 0.40595 5.22388
40 1T27 PCW 0.003373 0.4326 5.23256
41 4YGF AZM 0.003352 0.41951 5.23256
42 1DZT ATY 0.01865 0.41135 5.23256
43 4QJP V1F 0.001757 0.40905 5.23256
44 2Q8C AKG 0.02622 0.4057 5.23256
45 5FWE OGA 0.02808 0.40377 5.23256
46 5LY2 OGA 0.02967 0.40191 5.23256
47 3SAO NKN 0.00002634 0.44687 5.625
48 3VQ2 LP4 LP5 MYR DAO 0.002701 0.43688 5.81395
49 4Q0L V14 0.002513 0.41942 5.81395
50 4H6B 10Y 0.01479 0.40874 5.81395
51 5W0N UPU 0.02466 0.40578 5.81395
52 4H6B 10X 0.01469 0.40497 5.81395
53 3FW4 CAQ 0.001151 0.43192 6.39535
54 2WA4 069 0.004099 0.43157 6.39535
55 3W9K MYR 0.01482 0.40112 6.47482
56 4JH6 FCN 0.01303 0.41566 6.52174
57 2ET1 GLV 0.002162 0.46395 6.97674
58 2AXR ABL 0.005892 0.44091 6.97674
59 3ZGJ RMN 0.0164 0.41499 6.97674
60 5A3T MMK 0.005628 0.41038 6.97674
61 2GC0 PAN 0.006883 0.40928 6.97674
62 4PSB GA3 0.008076 0.40735 7.09677
63 1KTG AMP 0.02699 0.40793 7.24638
64 5L6G XYP 0.0006066 0.4937 7.55814
65 3WV6 GAL GLC 0.001258 0.44125 7.55814
66 3WV6 GAL BGC 0.003251 0.42921 7.55814
67 1ZB6 GST 0.002369 0.425 7.55814
68 3B6R ADP 0.006466 0.41415 7.55814
69 1ZB6 DIN 0.006004 0.40648 7.55814
70 3A6T 8OG 0.01131 0.40303 7.75194
71 4Q5H ANP 0.01092 0.40029 7.89474
72 4XCB AKG 0.006512 0.43578 8.13953
73 5DG2 GAL GLC 0.004662 0.4307 8.14815
74 1QY1 PRZ 0.00007562 0.48158 8.72093
75 1I06 TZL 0.0008633 0.48105 8.72093
76 4COQ SAN 0.003013 0.46047 8.72093
77 4WVO 3UZ 0.00171 0.4029 8.72093
78 1EPB REA 0.0000001748 0.62261 9.14634
79 2XMY CDK 0.005043 0.43943 9.30233
80 3AD8 FAD 0.008784 0.43077 9.30233
81 4WOE ADP 0.01789 0.41512 9.30233
82 1NVM OXL 0.02279 0.40709 9.30233
83 1ULE GLA GAL NAG 0.00015 0.52406 9.33333
84 5CJF 520 0.001299 0.45543 9.88372
85 3AMN CBK 0.007021 0.40074 9.88372
86 1ODM ASV 0.0004301 0.44969 10.4651
87 1LNM DTX 0.00261 0.42059 11.0465
88 1I7E IBS 0.01877 0.41698 11.6279
89 3FW3 ETS 0.0139 0.41006 11.6279
90 1OI6 TMP 0.01771 0.4161 12.7907
91 1C1L GAL BGC 0.008918 0.42239 13.1387
92 3RGA LSB 0.004348 0.42204 14.5349
93 4QPW XYP XYP XYP 0.001583 0.48532 15.493
94 2BO9 VAL 0.004157 0.44585 15.6977
95 5H9Q TD2 0.0000805 0.52733 16.129
96 2E27 AB0 0.005587 0.42513 16.8067
97 5NCF 8T5 0.006194 0.4369 20.354
98 3N9O OGA 0.03355 0.40136 23.8372
99 1DZK PRZ 0.001831 0.4392 24.8408
100 2GJ5 VD3 0.00004564 0.41494 32.0988
Pocket No.: 3; Query (leader) PDB : 2YG2; Ligand: S1P; Similar sites found: 36
This union binding pocket(no: 3) in the query (biounit: 2yg2.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2FB3 GTP 0.0111 0.40231 None
2 2A4W BLM 0.009642 0.40368 2.17391
3 2Z77 NCA 0.02038 0.40683 2.8777
4 4QDC ASD 0.003269 0.4004 2.90698
5 1VJ7 GDP 0.01162 0.41937 3.48837
6 4P7X AKG 0.00159 0.41711 3.48837
7 1F1V DHY 0.01121 0.41558 3.48837
8 1GP6 QUE 0.006537 0.40824 3.48837
9 1GP6 SIN 0.006811 0.40594 3.48837
10 5UI2 EQ3 0.01289 0.40425 3.48837
11 5FS0 5JC 0.01886 0.40427 4.06977
12 4D4U FUC NDG GAL FUC 0.01674 0.41158 4.65116
13 4GGZ BTN 0.01109 0.40746 5.21739
14 1OPB RET 0.008906 0.40435 5.22388
15 1OLM VTQ 0.009957 0.40026 5.23256
16 3T2W BTN 0.004149 0.43226 5.7377
17 3P3N AKG 0.02062 0.40521 6.39535
18 1H2M OGA 0.02105 0.40472 6.39535
19 1H2K OGA 0.02139 0.40428 6.39535
20 2OMN IPH 0.01101 0.4154 6.97674
21 4Y3O OGA 0.01804 0.40825 6.97674
22 2P1E LAC 0.01774 0.40575 6.97674
23 4CCN OGA 0.02413 0.40081 6.97674
24 4AZP A9M 0.003333 0.41775 7.97101
25 2X32 OTP 0.01132 0.41854 8.13953
26 3KRR DQX 0.01937 0.41696 8.72093
27 4BVA T3 0.01738 0.40359 9.30233
28 4GYI ADP 0.01394 0.40273 9.88372
29 1GT4 UNA 0.003625 0.40027 11.3208
30 1ERB ETR 0.003953 0.41927 12.2093
31 1ZHX HC3 0.004074 0.41719 12.2093
32 5C3R HMU 0.004206 0.41525 13.9535
33 5C3R AKG 0.004206 0.41525 13.9535
34 4X5S AZM 0.01293 0.42246 15.1163
35 5OO5 UUA 0.009398 0.40329 17.7419
36 3PUR 2HG 0.0291 0.40092 23.8372
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