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Receptor
PDB id Resolution Class Description Source Keywords
2E56 2 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF HUMAN MD-2 HOMO SAPIENS INNATE IMMUNITY LIPID-BINDING LIPID BINDING PROTEIN
Ref.: CRYSTAL STRUCTURES OF HUMAN MD-2 AND ITS COMPLEX WI ANTIENDOTOXIC LIPID IVA. SCIENCE V. 316 1632 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MYR A:501;
A:601;
A:701;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
228.371 C14 H28 O2 CCCCC...
NAG A:801;
A:901;
Invalid;
Invalid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2E56 2 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF HUMAN MD-2 HOMO SAPIENS INNATE IMMUNITY LIPID-BINDING LIPID BINDING PROTEIN
Ref.: CRYSTAL STRUCTURES OF HUMAN MD-2 AND ITS COMPLEX WI ANTIENDOTOXIC LIPID IVA. SCIENCE V. 316 1632 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 208 families.
1 2E59 - LP5 LP4 n/a n/a
2 2E56 - MYR C14 H28 O2 CCCCCCCCCC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 families.
1 2E59 - LP5 LP4 n/a n/a
2 2E56 - MYR C14 H28 O2 CCCCCCCCCC....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 42 families.
1 2E59 - LP5 LP4 n/a n/a
2 2E56 - MYR C14 H28 O2 CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MYR; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 EW8 1 1
3 TDA 1 1
4 F15 1 1
5 PLM 1 1
6 STE 1 1
7 X90 1 1
8 DAO 1 1
9 KNA 1 1
10 DCR 1 1
11 F23 1 1
12 11A 1 1
13 DKA 1 1
14 OCA 0.956522 1
15 SHV 0.833333 0.952381
16 KTC 0.793103 0.875
17 AZ1 0.73913 0.64
18 6NA 0.72 0.904762
19 ELA 0.71875 0.954545
20 OLA 0.71875 0.954545
21 NER 0.71875 0.954545
22 VCA 0.666667 0.954545
23 PAM 0.666667 0.954545
24 PML 0.625 0.6
25 3LA 0.606061 0.8
26 LEA 0.6 0.809524
27 MYZ 0.588235 0.909091
28 12H 0.586207 0.615385
29 ODD 0.567568 0.913043
30 BRC 0.566667 0.666667
31 14V 0.555556 0.740741
32 M12 0.545455 0.869565
33 14U 0.542857 0.703704
34 EIC 0.538462 0.913043
35 EOD 0.538462 0.7
36 D0G 0.5 0.954545
37 BMJ 0.5 0.954545
38 BNV 0.5 0.954545
39 BUA 0.48 0.666667
40 RCL 0.468085 0.84
41 FTT 0.459459 0.807692
42 HXD 0.459459 0.807692
43 56S 0.459459 0.653846
44 ODT 0.452381 0.782609
45 3X1 0.444444 0.818182
46 LNL 0.44186 0.826087
47 9J6 0.441176 0.666667
48 OOA 0.441176 0.76
49 CUY 0.435897 0.68
50 6UL 0.435897 0.68
51 CNS 0.435897 0.68
52 5UF 0.432432 0.807692
53 243 0.428571 0.807692
54 1QW 0.418605 0.606061
55 GYM 0.418605 0.606061
56 O8N 0.413793 0.75
57 1DO 0.413793 0.75
58 PL3 0.413793 0.75
59 OC9 0.413793 0.75
60 DE1 0.413793 0.75
61 F09 0.413793 0.75
62 T25 0.403846 0.677419
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2E56; Ligand: MYR; Similar sites found with APoc: 263
This union binding pocket(no: 1) in the query (biounit: 2e56.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 6GNO XDI None
2 3KFF ZBT None
3 3KFF XBT None
4 2AGC DAO None
5 5NFB 8VT None
6 6FOF LAT None
7 1NKI PPF None
8 1QFT HSM None
9 2CM4 RCL None
10 1QIN GIP None
11 2BS5 BGC GAL FUC None
12 6CZI 38E None
13 5T7I LAT NAG GAL None
14 4KYK IMN None
15 1DMY AZM None
16 6CAY ERG None
17 5CJF 520 None
18 4BCS BTN None
19 4CSD MFU None
20 4BJ8 BTN None
21 6F7X MFU None
22 5LJB RTL None
23 5HZ9 5M8 None
24 2GQR ADP None
25 1Y2F WAI None
26 3ZW2 NAG GAL FUC None
27 4FE2 AIR None
28 5D9G GLU ASN LEU TYR PHE GLN None
29 2AG4 LP3 1.38889
30 2AG4 OLA 1.38889
31 1X0P FAD 1.3986
32 2Z77 HE7 1.43885
33 4WVW SLT 2.08333
34 5GP0 GPP 2.08333
35 5O9W AKG 2.08333
36 2WBV SIA 2.08333
37 5MOB A8S 2.08333
38 2DIO EOD 2.08333
39 4U0W 16G 2.08333
40 3WW2 SF6 2.08333
41 5L2R MLA 2.08333
42 3TL1 JRO 2.08333
43 5BU3 4W9 2.08333
44 3WW2 LPK 2.08333
45 5CHR 4NC 2.18978
46 2P7Q GG6 2.25564
47 2OVD DAO 2.77778
48 5XEG AKG 2.77778
49 4RYV ZEA 2.77778
50 4JMO JAF 2.77778
51 5LUN OGA 2.77778
52 4ZSI 4R1 2.77778
53 4ZSI GLP 2.77778
54 5HZX 2GE 2.77778
55 3P7N FMN 2.77778
56 5B09 4MX 2.88462
57 1OPB RET 2.98507
58 5HZ5 65X 2.98507
59 4K55 H6P 3.22581
60 3SAO NKN 3.47222
61 5L6G XYP 3.47222
62 2YG2 FLC 3.47222
63 2YG2 S1P 3.47222
64 3R6K FUC GAL GLA 3.47222
65 5JSP DQY 3.47222
66 4MNS 2AX 3.47222
67 3HAV ATP 3.47222
68 5GM5 CBI 3.47222
69 5DKK FMN 3.47222
70 3X01 AMP 3.47222
71 1AUA BOG 3.47222
72 2R5V HHH 3.47222
73 1NYW DAU 3.47222
74 5KBE IPH 3.47222
75 3Q8G PEE 3.47222
76 5DG2 GAL GLC 3.7037
77 1FHW I5P 3.87597
78 4FFG 0U8 4.16667
79 1I7E IBS 4.16667
80 5TZO 7V7 4.16667
81 4XCB HY0 4.16667
82 1J3R 6PG 4.16667
83 4XCB AKG 4.16667
84 2GJ5 VD3 4.16667
85 6F6D AKG 4.16667
86 4MLO PAM 4.16667
87 1JG9 GLC 4.16667
88 1ULE GLA GAL NAG 4.16667
89 3NNF AKG 4.16667
90 1QY1 PRZ 4.16667
91 3WG3 A2G GAL NAG FUC 4.16667
92 3GFZ FMN 4.16667
93 5W0N UPU 4.16667
94 1OI6 TMP 4.16667
95 5BVB DOG 4.54545
96 3CM2 X23 4.61538
97 2HKA C3S 4.61538
98 3T50 FMN 4.6875
99 4OPC PGT 4.86111
100 4YLZ LAT NAG GAL 4.86111
101 3KDJ A8S 4.86111
102 2JIG PD2 4.86111
103 4MA6 28E 4.86111
104 4MZU TYD 4.86111
105 4OIC A8S 4.86111
106 4XZ3 ACP 4.86111
107 4ZU5 THM 4.86111
108 1M0W ANP 4.86111
109 5J3Z 6FQ 4.86111
110 2AXR ABL 4.86111
111 1GP6 QUE 4.86111
112 5OES ADP 4.86111
113 5FIT AP2 4.86111
114 4ZXA H8N 4.86111
115 3I8T LBT 4.86111
116 4OPC FDA 4.86111
117 2BWA GLC BGC 4.86111
118 1GP6 DH2 4.86111
119 1GP6 SIN 4.86111
120 5NLD LBT 5.03597
121 1SWG BTN 5.46875
122 3NMV PYV 5.55556
123 3RGA LSB 5.55556
124 6BYM HC3 5.55556
125 3E85 BSU 5.55556
126 3I4X DST 5.55556
127 5VNF VAL THR SER VAL VAL 5.55556
128 5LXB 7A9 5.55556
129 5V3D FCN 5.55556
130 1YKD CMP 5.55556
131 5KD6 6C7 5.55556
132 3QVI K95 5.55556
133 4GLW 0XT 5.55556
134 3PQB VGP 5.55556
135 1IS3 LAT 5.92593
136 3EW2 BTN 5.92593
137 2QL9 CIT 6.18557
138 2D6M LBT 6.25
139 4QCK ASD 6.25
140 4IAW LIZ 6.25
141 1N5S ADL 6.25
142 3R4Z GLA 6.25
143 4UYW H1S 6.25
144 4GQP B40 6.25
145 3UG4 AHR 6.25
146 4LED XXR 6.25
147 2YRX AMP 6.25
148 3AMN CBI 6.25
149 3AMN CBK 6.25
150 1NWW HPN 6.25
151 2HZQ STR 6.25
152 5KK4 44E 6.25
153 6HDT BTN 6.76692
154 3VV1 GAL FUC 6.875
155 5INJ 6C7 6.94444
156 4WOE ADP 6.94444
157 5MN0 A8S 6.94444
158 4NPL AKG 6.94444
159 6GR0 F8W 6.94444
160 4RFR RHN 6.94444
161 1UNB AKG 6.94444
162 3FW3 ETS 6.94444
163 1UNB PN1 6.94444
164 4J25 OGA 6.94444
165 5X7Q GLC GLC GLC GLC GLC 6.94444
166 5X7Q GLC GLC GLC GLC 6.94444
167 4WVO 3UZ 6.94444
168 5FXD H7Y 6.94444
169 1URX AAL GAL AAL GLA 6.94444
170 3NV3 GAL NAG MAN 7.24638
171 3WUC GLC GAL 7.29927
172 5KEW 6SB 7.44681
173 5TPV TYD 7.63889
174 5VKM GAL SIA 7.63889
175 1OKE BOG 7.63889
176 4OCT AKG 7.63889
177 2QK4 ATP 7.63889
178 2QX0 PH2 7.63889
179 2GC0 PAN 7.63889
180 3B6R ADP 7.63889
181 1N4K I3P 7.63889
182 3RWP ABQ 7.63889
183 6E08 NAP 7.63889
184 5TPU TYD 7.91367
185 5FPX GLY SER SER HIS HIS HIS HIS HIS 7.9646
186 2NZ5 226 8.33333
187 4DS8 A8S 8.33333
188 4KSY 1SY 8.33333
189 1Q23 FUA 8.33333
190 4OJ8 AKG 8.33333
191 5JO1 6LM 8.33333
192 1C1L GAL BGC 8.75912
193 1A78 TDG 8.95522
194 1OH2 SUC 9.02778
195 2WA4 069 9.02778
196 1LRH NLA 9.02778
197 2HFN FMN 9.02778
198 4JX1 CAH 9.02778
199 3N2O AG2 9.02778
200 4P42 PEE 9.02778
201 2Z6D FMN 9.23077
202 1TW4 CHD 9.6
203 3WV6 GAL BGC 9.72222
204 3WV6 GAL GLC 9.72222
205 4G7A AZM 9.72222
206 3HRD NIO 9.72222
207 5C3R AKG 9.72222
208 5C3R HMU 9.72222
209 3CF6 SP1 9.72222
210 1NSZ GLC 9.72222
211 3N0Y APC 9.72222
212 1T27 PCW 9.72222
213 1W2D ADP 9.72222
214 2ZHL NAG GAL GAL NAG 9.72222
215 2A1L PCW 9.72222
216 1ZM1 BGC BGC BGC 9.72222
217 5H9Q TD2 10.4167
218 5I0U DCY 10.4167
219 3W9R A8S 10.4167
220 5EO8 TFU 10.4167
221 3BRN SRO 10.4167
222 4W9N TCL 10.4167
223 6D50 GCB 10.4167
224 2QYK NPV 11.1111
225 6FXR AKG 11.1111
226 1LSH PLD 11.1111
227 5W3Y ACO 11.1111
228 3ZXE PGZ 11.2782
229 4ZU4 4TG 11.8056
230 6F5U CQN 11.8056
231 5KWY C3S 12.0301
232 3QRC SCR 12.5
233 4QM9 CYS 12.5
234 2OVW CBI 12.5
235 2R0H CTO 12.5
236 4GGZ BTN 13.0435
237 4LO6 SIA GAL 13.1944
238 2VFT SOR 13.1944
239 4QDF 30Q 13.1944
240 4LIT AKG 13.1944
241 4NS0 PIO 13.5338
242 4Y24 TD2 13.8889
243 5FU3 BGC BGC BGC 14.1509
244 1SLT NDG GAL 14.9254
245 1W6O LAT 14.9254
246 1GZW GAL BGC 14.9254
247 3OYW TDG 14.9254
248 5GLT BGC GAL NAG GAL 15.2778
249 6A56 LAT 15.2778
250 5K21 6QF 15.6028
251 6D61 4AA 15.9722
252 5AIG VPR 16.8
253 1ODM ASV 17.3611
254 5ML3 DL3 17.3611
255 5LX9 OLB 18.0556
256 1NJJ GET 18.0556
257 4JH6 FCN 18.8406
258 1KQW RTL 19.403
259 4BPZ GLC BGC BGC 19.4444
260 1B4P GPS 20.8333
261 5TBM 79A 21.7391
262 3MTX PGT 36.1111
263 5EZU MYR 38.2022
Pocket No.: 2; Query (leader) PDB : 2E56; Ligand: MYR; Similar sites found with APoc: 31
This union binding pocket(no: 2) in the query (biounit: 2e56.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 3GM5 CIT None
2 1OGX EQU None
3 1Y9Q MED None
4 5BVS EIC None
5 5HV0 AKG 1.38889
6 6BHQ NAG NAG FUL BMA MAN MAN NAG GAL 2.08333
7 2X34 UQ8 2.08333
8 3K4Z CBI 2.08333
9 2VGD XYP XYP XYP FX3 2.08333
10 2FCU AKG 2.77778
11 3B00 16A 2.77778
12 5EW9 5VC 2.77778
13 3W68 VIV 2.77778
14 5MBC FMN 3.47222
15 1LOP SIN ALA PRO ALA NIT 3.47222
16 2PR5 FMN 3.78788
17 4X5S AZM 4.16667
18 6BSX E7S 4.86111
19 4COQ SAN 5.55556
20 4D52 GIV 6.25
21 5NDB 8TW 6.94444
22 2VQ5 HBA 7.63889
23 5H5A 6OU 7.63889
24 5I8T LAC 7.63889
25 5VGS 9A4 9.02778
26 3K5I ADP 9.72222
27 3T2W BTN 9.83607
28 1U18 HSM 11.8056
29 5LWY OLB 14.5833
30 5VZ0 ADP 16.6667
31 4M26 AKG 19.4444
Pocket No.: 3; Query (leader) PDB : 2E56; Ligand: MYR; Similar sites found with APoc: 49
This union binding pocket(no: 3) in the query (biounit: 2e56.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 2AGC MYR None
2 1ZZ7 S0H None
3 1X8D RNS None
4 3SCH TB6 None
5 1OGZ EQU None
6 3NKS ACJ None
7 2XN5 FUN 2.08333
8 3A16 PXO 2.77778
9 1MDC PLM 3.0303
10 4GCZ FMN 3.47222
11 3HX3 RET 3.47222
12 4YGF AZM 3.47222
13 5SVV FMN 3.64964
14 1Y7P RIP 4.16667
15 5NEA 8V8 4.16667
16 5N0L ILE 4.16667
17 2X05 X05 4.16667
18 5IXH OTP 4.16667
19 4WUJ FMN 4.86111
20 3JU6 ANP 4.86111
21 6GG9 FMN 4.86111
22 4RDL FUC GAL NDG FUC 5.55556
23 3FW9 SLX 5.55556
24 3TTZ 07N 5.55556
25 2OZ5 7XY 5.55556
26 2YMZ LAT 6.15385
27 2ZMF CMP 6.94444
28 5A61 3PO 6.94444
29 4UDK BMA NDG 6.94444
30 5FQK 6NT 6.94444
31 2IUW AKG 8.33333
32 2XXP DSL 8.33333
33 4OCX MT1 8.33333
34 1RJW ETF 8.33333
35 2PA7 TYD 8.51064
36 2Z6C FMN 8.52713
37 5DJT FMN 9.02778
38 5DJU FMN 9.02778
39 4D06 NAR 9.02778
40 3H22 B53 9.02778
41 3ZO7 K6H 9.57447
42 2GWH PCI 9.72222
43 1FMB HYB 10.5769
44 2ET1 GLV 11.1111
45 3WUD GLC GAL 11.7647
46 4M1U A2G MBG 12.5
47 5FS0 5JC 15.9722
48 5EFW FMN 23.3333
49 5DYO FLU 31.9444
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