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Receptor
PDB id Resolution Class Description Source Keywords
3MTX 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CHICKEN MD-1 GALLUS GALLUS MD-1 LY86 RP105 ASSOCIATED PROTEIN IMMUNE SYSTEM
Ref.: CRYSTAL STRUCTURE OF SOLUBLE MD-1 AND ITS INTERACTI LIPID IVA. PROC.NATL.ACAD.SCI.USA V. 107 10990 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:1;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PGE A:1;
Invalid;
none;
submit data
150.173 C6 H14 O4 C(COC...
PGT A:300;
B:300;
Valid;
Valid;
none;
none;
submit data
751.023 C40 H79 O10 P CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3MTX 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CHICKEN MD-1 GALLUS GALLUS MD-1 LY86 RP105 ASSOCIATED PROTEIN IMMUNE SYSTEM
Ref.: CRYSTAL STRUCTURE OF SOLUBLE MD-1 AND ITS INTERACTI LIPID IVA. PROC.NATL.ACAD.SCI.USA V. 107 10990 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3MU3 - LP4 LP5 n/a n/a
2 3MTX - PGT C40 H79 O10 P CCCCCCCCCC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 3MU3 - LP4 LP5 n/a n/a
2 3MTX - PGT C40 H79 O10 P CCCCCCCCCC....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 3MU3 - LP4 LP5 n/a n/a
2 3MTX - PGT C40 H79 O10 P CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PGT; Similar ligands found: 107
No: Ligand ECFP6 Tc MDL keys Tc
1 PGT 1 1
2 LHG 1 1
3 CD4 0.870968 0.954545
4 44G 0.868852 1
5 D3D 0.867647 0.977778
6 PGW 0.867647 0.977778
7 DR9 0.855072 0.977778
8 PGV 0.855072 0.977778
9 PGK 0.842857 0.93617
10 P6L 0.842857 0.977778
11 OZ2 0.830986 0.977778
12 DGG 0.808219 0.93617
13 CN3 0.771429 0.954545
14 PTY 0.746269 0.826923
15 PEV 0.746269 0.826923
16 PEH 0.746269 0.826923
17 8PE 0.746269 0.826923
18 PEF 0.746269 0.826923
19 CN6 0.742857 0.954545
20 P5S 0.73913 0.843137
21 PEE 0.735294 0.811321
22 9PE 0.735294 0.826923
23 HGX 0.714286 0.701754
24 PC7 0.714286 0.701754
25 LIO 0.714286 0.701754
26 PLD 0.714286 0.701754
27 HGP 0.714286 0.701754
28 6PL 0.714286 0.701754
29 3PH 0.703125 0.911111
30 7PH 0.703125 0.911111
31 LPP 0.703125 0.911111
32 6PH 0.703125 0.911111
33 F57 0.703125 0.911111
34 PX8 0.692308 0.888889
35 7P9 0.692308 0.911111
36 PX2 0.692308 0.888889
37 AGA 0.666667 0.955556
38 XP5 0.661972 0.701754
39 LOP 0.657895 0.811321
40 L9Q 0.657895 0.811321
41 6OU 0.657895 0.811321
42 PII 0.648649 0.84
43 CDL 0.647887 0.866667
44 PD7 0.646154 0.911111
45 P50 0.64557 0.807692
46 PSF 0.633803 0.843137
47 TGL 0.633333 0.659091
48 PCW 0.632911 0.689655
49 ZPE 0.620253 0.811321
50 PCK 0.617284 0.666667
51 M7U 0.616438 0.911111
52 D21 0.616438 0.891304
53 PIF 0.61039 0.823529
54 P3A 0.609756 0.934783
55 PIZ 0.6 0.803922
56 GP7 0.595238 0.811321
57 FAW 0.59375 0.704545
58 L2C 0.59375 0.704545
59 DGA 0.59375 0.704545
60 DDR 0.59375 0.704545
61 44E 0.590909 0.911111
62 PEK 0.590361 0.811321
63 IP9 0.5875 0.803922
64 52N 0.5875 0.823529
65 PIO 0.5875 0.823529
66 PSC 0.581395 0.689655
67 B7N 0.578313 0.823529
68 3PE 0.565789 0.75
69 MC3 0.551282 0.660714
70 PCF 0.551282 0.660714
71 PC1 0.551282 0.660714
72 GYM 0.539683 0.727273
73 1QW 0.539683 0.727273
74 PDK 0.537634 0.716667
75 LBR 0.535211 0.652174
76 LPC 0.526316 0.736842
77 LAP 0.526316 0.736842
78 LP3 0.526316 0.736842
79 PGM 0.520548 0.933333
80 PIE 0.517241 0.769231
81 T7X 0.516484 0.823529
82 NKO 0.507246 0.911111
83 NKN 0.507246 0.911111
84 2JT 0.5 0.666667
85 G2A 0.5 0.666667
86 EPH 0.5 0.811321
87 POV 0.494253 0.649123
88 L9R 0.494253 0.649123
89 S12 0.493976 0.807692
90 SQD 0.482759 0.640625
91 CN5 0.481013 0.933333
92 OLB 0.472222 0.711111
93 OLC 0.472222 0.711111
94 42H 0.470588 0.724138
95 DGD 0.467391 0.618182
96 1O2 0.456522 0.6
97 MVC 0.452055 0.711111
98 3TF 0.451613 0.6
99 NKP 0.448718 0.891304
100 PCJ 0.44186 0.607143
101 78N 0.438356 0.711111
102 78M 0.438356 0.711111
103 DLP 0.43617 0.649123
104 1L2 0.42 0.6
105 DB4 0.402439 0.764706
106 PBU 0.4 0.764706
107 GGD 0.4 0.607143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3MTX; Ligand: PGT; Similar sites found with APoc: 304
This union binding pocket(no: 1) in the query (biounit: 3mtx.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 6GNO XDI None
2 2D6M LBT None
3 4L4J NAG NAG BMA MAN NAG None
4 5DG2 GAL GLC None
5 5FUI APY None
6 1SLT NDG GAL None
7 3ZW0 FUC None
8 2GJ5 VD3 None
9 3WUC GLC GAL None
10 4ZSI 4R1 None
11 4TW7 37K None
12 1KGI T4A None
13 1OIJ AKG None
14 4ZSI GLP None
15 5HWV MBN None
16 6FOF LAT None
17 6D6L FY4 None
18 1TT8 PHB None
19 3ZW2 GAL FUC None
20 5VKM GAL SIA None
21 4GGL CJC None
22 2E5Y ATP None
23 3OYW TDG None
24 3ZW2 NAG GAL FUC None
25 5ODY 9SK None
26 1P0Z FLC None
27 1SDW IYT None
28 5N0L ILE 1.3245
29 4U0W 16G 1.3245
30 1VKF CIT 1.3245
31 4EKV BTN 1.3245
32 1ZNY GDP 1.3245
33 3NV3 GAL NAG MAN 1.44928
34 6A63 LAT 1.44928
35 6FA4 D1W 1.98676
36 2PTM CMP 1.98676
37 3PNA CMP 1.98676
38 2BP1 FLC 1.98676
39 3B1Q NOS 1.98676
40 1RYD GLC 1.98676
41 4Y24 TD2 1.98676
42 5C8W PCG 2.0979
43 4QPW XYP XYP XYP 2.11268
44 4XQM MAN 2.12766
45 1GZW GAL BGC 2.23881
46 4CPH LH4 2.3622
47 5OO5 UUA 2.41935
48 4RF7 ARG 2.64901
49 5JSP DQY 2.64901
50 2OMN IPH 2.64901
51 3E2M E2M 2.64901
52 4D06 NAR 2.64901
53 4COQ SAN 2.64901
54 5LHT TIH 2.64901
55 2CJ9 SSA 2.64901
56 1NE6 SP1 2.64901
57 2RDQ AKG 2.64901
58 5FWJ MMK 2.64901
59 4UHL VFV 2.64901
60 4EE7 PIS 2.64901
61 3A6T 8OG 3.10078
62 1Y52 BTN 3.1746
63 4BCS BTN 3.2
64 5I0U DCY 3.31126
65 5TPV TYD 3.31126
66 2ET1 GLV 3.31126
67 2CDO GAL AAL GAL AAL GAL AAL 3.31126
68 6EWZ APC 3.31126
69 6E08 NAP 3.31126
70 1YFS ALA 3.31126
71 2X32 OTP 3.31126
72 2X34 UQ8 3.31126
73 3ALN ANP 3.31126
74 3ZDS OMD 3.31126
75 5FQK 6NT 3.31126
76 4FFG 0U8 3.31126
77 3VSV XYP 3.31126
78 3PQB VGP 3.31126
79 2PNC CLU 3.31126
80 4NG2 OHN 3.53982
81 2AG4 LP3 3.97351
82 2AG4 OLA 3.97351
83 1KTC NGA 3.97351
84 1UNB AKG 3.97351
85 1ZZ7 S0H 3.97351
86 1EX7 5GP 3.97351
87 1UNB PN1 3.97351
88 4WOE ADP 3.97351
89 1I82 BGC BGC 3.97351
90 6GR0 F8W 3.97351
91 3FW4 CAQ 3.97351
92 5KO1 6UY 3.97351
93 1ZDQ MSM 3.97351
94 3ZJX BOG 3.97351
95 5N53 8NB 3.97351
96 4QRH 0O2 3.97351
97 5XQW 8EU 3.97351
98 3OCP CMP 4.31655
99 1WKL ATP 4.37956
100 5LJB RTL 4.44444
101 1OGX EQU 4.58015
102 4NPL AKG 4.63576
103 5NFB 8VT 4.63576
104 5TZO 7V7 4.63576
105 3VMG 9CA 4.63576
106 1TQP ATP 4.63576
107 4G7A AZM 4.63576
108 4H6B 10X 4.63576
109 5HV0 AKG 4.63576
110 1DZK PRZ 4.63576
111 4ZXA H8N 4.63576
112 3V8S 0HD 4.63576
113 3FW3 ETS 4.63576
114 1F5F DHT 4.63576
115 2VC9 NOK 4.63576
116 4CCW VKC 4.63576
117 1U6R ADP 4.63576
118 2PVF ACP 4.63576
119 5C3R AKG 4.63576
120 5C3R HMU 4.63576
121 5VAD PRO 4.63576
122 4IMO PWZ 4.63576
123 4ZS4 ATP 4.63576
124 6F4T OGA 4.63576
125 1OGZ EQU 4.8
126 5Y4R C2E 4.82759
127 2ZSC BTN 4.96454
128 3WUD GLC GAL 5.14706
129 1IS3 LAT 5.18518
130 1NKI PPF 5.18518
131 5O9W AKG 5.29801
132 2IUW AKG 5.29801
133 1J3R 6PG 5.29801
134 5L6G XYP 5.29801
135 4X5S AZM 5.29801
136 6F6D AKG 5.29801
137 4FE2 AIR 5.29801
138 1W96 S1A 5.29801
139 2GC0 PAN 5.29801
140 3S7D SAH 5.29801
141 6EJ7 UDX 5.29801
142 4XCB AKG 5.29801
143 3AJH BL3 5.29801
144 1ULE GLA GAL NAG 5.33333
145 2YMZ LAT 5.38462
146 6CED EYA 5.60748
147 3SAO DBH 5.96026
148 3JU6 ANP 5.96026
149 4RFR RHN 5.96026
150 3SAO NKN 5.96026
151 2VFT SOR 5.96026
152 3RGA LSB 5.96026
153 1NYW DAU 5.96026
154 1T27 PCW 5.96026
155 4RD0 GDP 5.96026
156 3O2K DST 5.96026
157 6FXR AKG 5.96026
158 4YVN EBS 5.96026
159 5FXD H7Y 5.96026
160 5LY1 PPI 5.96026
161 4NVP 7CH 5.96026
162 1U0A BGC BGC BGC BGC 5.96026
163 5KR7 6X9 5.96026
164 4QCK ASD 5.96026
165 5GP0 GPP 6.04027
166 2CJU PHX 6.19469
167 1OFZ FUC 6.62252
168 1VRP ADP 6.62252
169 4HWT 1B2 6.62252
170 2AXR ABL 6.62252
171 2GQS C2R 6.62252
172 2Z5Y HRM 6.62252
173 6FBZ MGP 6.62252
174 5VCM UDP 6.62252
175 2GQS ADP 6.62252
176 4BG4 ADP 6.62252
177 2P7Q GG6 6.76692
178 6D61 4AA 7.28477
179 3FW9 SLX 7.28477
180 5H9Q TD2 7.28477
181 3WV6 GAL GLC 7.28477
182 3WV6 GAL BGC 7.28477
183 4CSD MFU 7.28477
184 4GN8 ASO 7.28477
185 4KU7 PCG 7.28477
186 1Y9Q MED 7.28477
187 3SHR CMP 7.28477
188 3Q60 ATP 7.28477
189 1ODM ASV 7.28477
190 2QK4 ATP 7.28477
191 2XUM OGA 7.28477
192 3L5R 47X 7.37705
193 1C5C TK4 7.44186
194 1QKQ MAN 7.74648
195 5XEG AKG 7.94702
196 3RWP ABQ 7.94702
197 2FCU AKG 7.94702
198 1K0E TRP 7.94702
199 6CC0 EWM 7.94702
200 1Z03 OCH 7.94702
201 3HQP OXL 7.94702
202 1NWW HPN 8.05369
203 3G08 FEE 8.08081
204 3RUG DB6 8.08081
205 4ZU4 4TG 8.10811
206 5JAX 6J7 8.14815
207 3ZXE PGZ 8.27068
208 43CA NPO 8.54701
209 5T7I LAT NAG GAL 8.60927
210 3H55 GLA 8.60927
211 1Y2F WAI 8.63309
212 4JH6 FCN 8.69565
213 1LSH PLD 9.27152
214 3JQ3 ADP 9.27152
215 3WG3 A2G GAL NAG FUC 9.27152
216 3KDM TES 9.27152
217 4M26 AKG 9.27152
218 1I1Q TRP 9.27152
219 5LRT ADP 9.27152
220 1C1L GAL BGC 9.48905
221 5B09 4MX 9.61539
222 1OPB RET 9.70149
223 4QYN RTL 9.77444
224 2AGC DAO 9.93377
225 4OPC PGT 9.93377
226 4OPC FDA 9.93377
227 5XLY C2E 9.93377
228 1H8S AIC 9.93377
229 1GP6 SIN 9.93377
230 1GP6 DH2 9.93377
231 1GP6 QUE 9.93377
232 4WVW SLT 10.4167
233 1A78 TDG 10.4478
234 1GT4 UNA 10.596
235 4LIT AKG 10.596
236 5GLT BGC GAL NAG GAL 10.596
237 1NX0 ALA LYS ALA ILE ALA 10.596
238 2FUE M1P 10.596
239 5G48 1FL 10.596
240 4D52 GIV 10.596
241 2YAB AMP 10.596
242 4D52 GXL 10.596
243 2XMY CDK 10.596
244 4D4U FUC GAL NAG 10.596
245 3NNT DQA 10.596
246 4H2X G5A 10.6796
247 1AUA BOG 11.2583
248 1OS7 AKG 11.2583
249 5UC4 83S 11.2583
250 1LFO OLA 11.7188
251 5X7Q GLC GLC GLC GLC GLC 11.9205
252 5X7Q GLC GLC GLC GLC 11.9205
253 1DZT TPE 11.9205
254 5ML3 DL3 12.0805
255 2BS5 BGC GAL FUC 12.2222
256 5KJW 53C 12.5828
257 4N14 WR7 12.5828
258 5OCQ 9RN G4S 9RN G4S 12.5828
259 1QY1 PRZ 13.245
260 2YKL NLD 13.245
261 4MOB ADP 13.245
262 6B9T 2HE 13.245
263 1I06 TZL 13.245
264 2R5V HHH 13.245
265 3EWK FAD 13.245
266 6F7X MFU 13.3333
267 4YZ5 SLT 13.9073
268 4OCT AKG 13.9073
269 1UMZ BGC BGC XYS BGC XYS GAL 13.9073
270 2ZHL NAG GAL GAL NAG 14.1892
271 4H2V AMP 14.5455
272 3PUR 2HG 14.5695
273 5JZJ AN2 14.5695
274 4P7X AKG 15.2318
275 4P7X YCP 15.2318
276 2V73 SIA 15.2318
277 1S68 AMP 15.2318
278 2NZ2 CIR 15.2318
279 5H9P TD2 15.894
280 1YKD CMP 15.894
281 2C49 ADN 16.5563
282 4CLO XP0 17.2185
283 1OFL NGK GCD 17.2185
284 5L2R MLA 17.8808
285 4Q5H ANP 18.4211
286 4YLZ LAT NAG GAL 18.543
287 4YGF AZM 19.2053
288 1OI6 TMP 19.8675
289 4QDF 30Q 20.5298
290 4QDC ASD 20.5298
291 1PVC ILE SER GLU VAL 22.5166
292 1MEX RAC 22.5166
293 1N5S ADL 23.2143
294 5VNF VAL THR SER VAL VAL 24.5033
295 5XIO HFG 25.8278
296 4WO4 JLS 27
297 3AVR OGA 27.2727
298 4L4V 1VY 27.2727
299 5U98 1KX 27.2727
300 2VL1 GLY GLY 32.4503
301 3VQ2 LP4 LP5 MYR DAO 33.3333
302 5AN1 GSH 35.7616
303 2E56 MYR 36.1111
304 1MDC PLM 37.1212
Pocket No.: 2; Query (leader) PDB : 3MTX; Ligand: PGT; Similar sites found with APoc: 70
This union binding pocket(no: 2) in the query (biounit: 3mtx.bio2) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 4JNJ BTN None
2 3A76 SPD None
3 3ZW2 GLA NAG GAL FUC None
4 2CHT TSA None
5 4BJ8 BTN None
6 3ZO7 K6H None
7 1QIN GIP None
8 2ARC ARA None
9 5FPE 3TR 1.3245
10 1R5L VIV 1.3245
11 3BGD PM6 1.3245
12 3EW2 BTN 1.48148
13 2UZ2 BTN 1.53846
14 2QX0 PH2 2.64901
15 4BIX ADP 2.64901
16 6HDT BTN 3.7594
17 3CBC DBS 3.97351
18 5ZMY TAR 3.97351
19 1O6U PLM 3.97351
20 6CAY ERG 3.97351
21 2VQ5 HBA 4.63576
22 3EVF GTA 4.63576
23 5OX6 A1Z 4.63576
24 5H9Y BGC BGC BGC BGC 4.63576
25 5NLD LBT 5.03597
26 3B6R ADP 5.29801
27 2IXC TRH 5.29801
28 5C5T AKG 5.29801
29 1NX4 AKG 5.29801
30 1IND EOT 5.96026
31 4EKQ NPO 5.96026
32 4OJ8 AKG 5.96026
33 1T36 ORN 5.96026
34 1BHX ASP PHE GLU GLU ILE 6.12245
35 3UB7 ACM 6.62252
36 2GQR ADP 6.62252
37 1WBI BTN 6.97674
38 2HRL SIA GAL SIA BGC NGA CEQ 7.08661
39 2WA4 069 7.28477
40 3P5P A3C 7.28477
41 6C0T EE4 7.28477
42 5KBF CMP 8.60927
43 3WW2 LPK 8.60927
44 5K8S CMP 8.78378
45 1WW5 SGA BGC 9.27152
46 4C2C ALA ALA ALA 9.27152
47 4CJN QNZ 9.27152
48 1X14 NAD 9.27152
49 5OC1 ANN 9.93377
50 1TW4 CHD 10.4
51 4D4U FUC GAL NDG FUC 10.596
52 5AIG VPR 11.2
53 3DAK ANP 12.5828
54 1GQG DCD 12.5828
55 3C0G 3AM 12.5828
56 2QL9 CIT 13.4021
57 3SLS 77D 13.9073
58 3N9P OGA 14.5695
59 3A23 GAL 14.5695
60 3N9O OGA 14.5695
61 3N9Q OGA 14.5695
62 4C2W ANP 17.3077
63 4KBA 1QM 17.8808
64 5OKT 9XK 17.8808
65 1ELI PYC 18.543
66 3B00 16A 20.5298
67 2JIG PD2 21.1921
68 1DMY AZM 23.8411
69 1FUR MLT 25.8278
70 5ZCO CHD 30.6122
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