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 1256 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 1068 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 922 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: 97
No: Ligand ECFP6 Tc MDL keys Tc
1 LHG 1 1
2 PGT 1 1
3 CD4 0.870968 0.954545
4 44G 0.868852 1
5 PGW 0.867647 0.977778
6 DR9 0.855072 0.977778
7 PGV 0.855072 0.977778
8 PGK 0.842857 0.93617
9 P6L 0.842857 0.977778
10 OZ2 0.830986 0.977778
11 DGG 0.808219 0.93617
12 CN3 0.771429 0.954545
13 PEH 0.746269 0.826923
14 PTY 0.746269 0.826923
15 PEF 0.746269 0.826923
16 PEV 0.746269 0.826923
17 8PE 0.746269 0.826923
18 CN6 0.742857 0.954545
19 P5S 0.73913 0.843137
20 PEE 0.735294 0.811321
21 9PE 0.735294 0.826923
22 LIO 0.714286 0.701754
23 HGP 0.714286 0.701754
24 PLD 0.714286 0.701754
25 6PL 0.714286 0.701754
26 HGX 0.714286 0.701754
27 PC7 0.714286 0.701754
28 7PH 0.703125 0.911111
29 LPP 0.703125 0.911111
30 3PH 0.703125 0.911111
31 6PH 0.703125 0.911111
32 7P9 0.692308 0.911111
33 PX2 0.692308 0.888889
34 AGA 0.666667 0.955556
35 XP5 0.661972 0.701754
36 LOP 0.657895 0.811321
37 L9Q 0.657895 0.811321
38 PII 0.648649 0.84
39 CDL 0.647887 0.866667
40 PD7 0.646154 0.911111
41 PSF 0.633803 0.843137
42 TGL 0.633333 0.659091
43 PCW 0.632911 0.689655
44 ZPE 0.620253 0.811321
45 PCK 0.617284 0.666667
46 M7U 0.616438 0.911111
47 PIF 0.61039 0.823529
48 P3A 0.609756 0.934783
49 PIZ 0.6 0.803922
50 GP7 0.595238 0.811321
51 L2C 0.59375 0.704545
52 DGA 0.59375 0.704545
53 DDR 0.59375 0.704545
54 44E 0.590909 0.911111
55 PEK 0.590361 0.811321
56 PIO 0.5875 0.823529
57 IP9 0.5875 0.803922
58 52N 0.5875 0.823529
59 PSC 0.581395 0.689655
60 B7N 0.578313 0.823529
61 3PE 0.565789 0.75
62 MC3 0.551282 0.660714
63 PC1 0.551282 0.660714
64 PCF 0.551282 0.660714
65 GYM 0.539683 0.727273
66 PDK 0.537634 0.716667
67 LBR 0.535211 0.652174
68 LP3 0.526316 0.736842
69 LPC 0.526316 0.736842
70 LAP 0.526316 0.736842
71 PGM 0.520548 0.933333
72 PIE 0.517241 0.769231
73 T7X 0.516484 0.823529
74 NKN 0.507246 0.911111
75 EPH 0.5 0.811321
76 2JT 0.5 0.666667
77 G2A 0.5 0.666667
78 L9R 0.494253 0.649123
79 S12 0.493976 0.807692
80 SQD 0.482759 0.640625
81 CN5 0.481013 0.933333
82 OLB 0.472222 0.711111
83 OLC 0.472222 0.711111
84 42H 0.470588 0.724138
85 DGD 0.467391 0.618182
86 1O2 0.456522 0.6
87 MVC 0.452055 0.711111
88 3TF 0.451613 0.6
89 NKP 0.448718 0.891304
90 PCJ 0.44186 0.607143
91 78N 0.438356 0.711111
92 78M 0.438356 0.711111
93 DLP 0.43617 0.649123
94 1L2 0.42 0.6
95 DB4 0.402439 0.764706
96 GGD 0.4 0.607143
97 PBU 0.4 0.764706
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3MTX; Ligand: PGT; Similar sites found: 208
This union binding pocket(no: 1) in the query (biounit: 3mtx.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2D6M LBT 0.0008226 0.48365 None
2 4L4J NAG NAG BMA MAN NAG 0.0009171 0.48026 None
3 5DG2 GAL GLC 0.000323 0.47716 None
4 1SN0 T44 0.00214 0.45746 None
5 5FUI APY 0.002291 0.45632 None
6 1SLT NDG GAL 0.00522 0.44485 None
7 3ZW0 FUC 0.008465 0.44436 None
8 4ZSI 4R1 0.005483 0.42914 None
9 4TW7 37K 0.001336 0.42845 None
10 1OIJ AKG 0.01572 0.42252 None
11 4ZSI GLP 0.007787 0.42192 None
12 2WZ5 MET 0.00709 0.42072 None
13 5HWV MBN 0.0212 0.41993 None
14 1TT8 PHB 0.002711 0.416 None
15 1KGI T4A 0.0038 0.41588 None
16 3ZW2 GAL FUC 0.01575 0.41446 None
17 3IX8 TX3 0.003091 0.41369 None
18 4GGL CJC 0.01488 0.41203 None
19 3OYW TDG 0.034 0.40886 None
20 3ZW2 NAG GAL FUC 0.01846 0.40746 None
21 4JNJ BTN 0.02088 0.40485 None
22 1P0Z FLC 0.04673 0.40089 None
23 1SDW IYT 0.03011 0.4004 None
24 4U0W 16G 0.009398 0.41454 1.3245
25 1VKF CIT 0.03358 0.407 1.3245
26 1ZNY GDP 0.04407 0.40275 1.3245
27 3PNA CMP 0.02632 0.41077 1.98676
28 2BP1 FLC 0.02546 0.40722 1.98676
29 3B1Q NOS 0.01241 0.40571 1.98676
30 4Y24 TD2 0.03148 0.40294 1.98676
31 5C8W PCG 0.01705 0.42066 2.0979
32 4QPW XYP XYP XYP 0.003181 0.4303 2.11268
33 4XQM MAN 0.02187 0.41445 2.12766
34 1GZW GAL BGC 0.0228 0.40512 2.23881
35 4CPH LH4 0.02545 0.40065 2.3622
36 5OO5 UUA 0.006709 0.42499 2.41935
37 5JSP DQY 0.0148 0.4298 2.64901
38 2OMN IPH 0.01397 0.42951 2.64901
39 3E2M E2M 0.001576 0.42868 2.64901
40 2RDQ AKG 0.005092 0.41665 2.64901
41 5FWJ MMK 0.02413 0.41275 2.64901
42 3QP8 HL0 0.01548 0.40445 2.64901
43 2CJ9 SSA 0.01404 0.40327 2.64901
44 4EE7 PIS 0.04697 0.40079 2.64901
45 3A6T 8OG 0.01343 0.41066 3.10078
46 5I0U DCY 0.002979 0.45507 3.31126
47 5TPV TYD 0.005578 0.45467 3.31126
48 2CDO GAL AAL GAL AAL GAL AAL 0.01563 0.43944 3.31126
49 1YFS ALA 0.01327 0.42415 3.31126
50 3ALN ANP 0.01074 0.41528 3.31126
51 5FQK 6NT 0.03539 0.41019 3.31126
52 4FFG 0U8 0.01772 0.40993 3.31126
53 3VSV XYP 0.03509 0.4042 3.31126
54 2PNC CLU 0.04667 0.40401 3.31126
55 3PQB VGP 0.01181 0.40067 3.31126
56 4NG2 OHN 0.004638 0.40934 3.53982
57 4WOE ADP 0.004956 0.45481 3.97351
58 3CBC DBS 0.01541 0.42987 3.97351
59 1EX7 5GP 0.01713 0.4249 3.97351
60 1I82 BGC BGC 0.02347 0.4187 3.97351
61 3W8X FTK 0.01307 0.41851 3.97351
62 3FW4 CAQ 0.005122 0.40756 3.97351
63 5KO1 6UY 0.01564 0.40751 3.97351
64 4DE9 VTP 0.002439 0.40687 3.97351
65 1ZDQ MSM 0.04401 0.40581 3.97351
66 3ZJX BOG 0.04334 0.40491 3.97351
67 4QRH 0O2 0.01301 0.40174 3.97351
68 3OCP CMP 0.01376 0.42133 4.31655
69 5LJB RTL 0.003834 0.4254 4.44444
70 1OGX EQU 0.01142 0.41761 4.58015
71 4NPL AKG 0.002398 0.47252 4.63576
72 5NFB 8VT 0.004982 0.4509 4.63576
73 4G7A AZM 0.01228 0.434 4.63576
74 3VMG 9CA 0.007168 0.43146 4.63576
75 4BQY FNT 0.002806 0.43144 4.63576
76 1TQP ATP 0.002294 0.4251 4.63576
77 4H6B 10X 0.01096 0.42231 4.63576
78 5HV0 AKG 0.01012 0.42017 4.63576
79 5C3R AKG 0.00963 0.41405 4.63576
80 5C3R HMU 0.00963 0.41405 4.63576
81 4ZXA H8N 0.02585 0.41118 4.63576
82 3V8S 0HD 0.01528 0.408 4.63576
83 3FW3 ETS 0.01135 0.40749 4.63576
84 1DZK PRZ 0.01984 0.40594 4.63576
85 2VC9 NOK 0.02988 0.40411 4.63576
86 4CCW VKC 0.0341 0.40408 4.63576
87 2PVF ACP 0.01867 0.40385 4.63576
88 4HN1 TYD 0.03145 0.40296 4.63576
89 5VAD PRO 0.02292 0.40288 4.63576
90 4IMO PWZ 0.04288 0.402 4.63576
91 1NKI PPF 0.01458 0.42865 5.18518
92 1J3R 6PG 0.00951 0.42949 5.29801
93 4X5S AZM 0.01792 0.42658 5.29801
94 3ML5 AZM 0.02749 0.4161 5.29801
95 4FE2 AIR 0.01958 0.41351 5.29801
96 1W96 S1A 0.0115 0.41046 5.29801
97 3S7D SAH 0.01884 0.40703 5.29801
98 5C5T AKG 0.03217 0.40618 5.29801
99 4XCB AKG 0.04159 0.40412 5.29801
100 3AJH BL3 0.02203 0.40042 5.29801
101 2YMZ LAT 0.0009732 0.45324 5.38462
102 3SAO DBH 0.001696 0.48414 5.96026
103 3JU6 ANP 0.006226 0.4484 5.96026
104 4RFR RHN 0.001922 0.44254 5.96026
105 3SAO NKN 0.00731 0.4353 5.96026
106 2VFT SOR 0.009563 0.42937 5.96026
107 3RGA LSB 0.006064 0.42707 5.96026
108 1NYW DAU 0.005898 0.42043 5.96026
109 4YVN EBS 0.04109 0.4056 5.96026
110 5FXD H7Y 0.01837 0.40418 5.96026
111 1U0A BGC BGC BGC BGC 0.02162 0.4008 5.96026
112 5KR7 6X9 0.03019 0.40034 5.96026
113 2CJU PHX 0.03863 0.40921 6.19469
114 1OFZ FUC 0.01037 0.43885 6.62252
115 4HWT 1B2 0.004331 0.42652 6.62252
116 2AXR ABL 0.01608 0.4238 6.62252
117 2GQS C2R 0.01022 0.41995 6.62252
118 2Z5Y HRM 0.02218 0.41468 6.62252
119 1VRP ADP 0.01749 0.40861 6.62252
120 2GQS ADP 0.01615 0.40685 6.62252
121 4BG4 ADP 0.01472 0.40547 6.62252
122 3FW9 SLX 0.0005295 0.46794 7.28477
123 5H9Q TD2 0.002138 0.45632 7.28477
124 3WV6 GAL GLC 0.001638 0.44821 7.28477
125 3WV6 GAL BGC 0.002904 0.44308 7.28477
126 4CSD MFU 0.009937 0.44028 7.28477
127 4KU7 PCG 0.008932 0.42672 7.28477
128 3Q60 ATP 0.01042 0.4159 7.28477
129 1ODM ASV 0.003836 0.41274 7.28477
130 2QK4 ATP 0.02944 0.40821 7.28477
131 2XUM OGA 0.03825 0.4032 7.28477
132 1C5C TK4 0.03511 0.40945 7.44186
133 1QKQ MAN 0.0005031 0.52606 7.74648
134 2QO4 CHD 0.004096 0.40081 7.93651
135 2FCU AKG 0.009244 0.44087 7.94702
136 1K0E TRP 0.008822 0.42698 7.94702
137 4XBT 3ZQ 0.01197 0.40966 7.94702
138 1Z03 OCH 0.03443 0.40857 7.94702
139 4XBT FLC 0.01764 0.4018 7.94702
140 3HQP OXL 0.04174 0.40038 7.94702
141 4ZU4 4TG 0.0007622 0.4697 8.10811
142 5JAX 6J7 0.01408 0.40969 8.14815
143 3ZXE PGZ 0.007693 0.44496 8.27068
144 5T7I LAT NAG GAL 0.01751 0.42688 8.60927
145 1Y2F WAI 0.00624 0.44623 8.63309
146 4JH6 FCN 0.003522 0.45632 8.69565
147 3JQ3 ADP 0.00995 0.42849 9.27152
148 3WG3 A2G GAL NAG FUC 0.03086 0.40713 9.27152
149 3KDM TES 0.04032 0.40512 9.27152
150 4M26 AKG 0.04644 0.40278 9.27152
151 1I1Q TRP 0.038 0.40236 9.27152
152 5LRT ADP 0.007452 0.40083 9.27152
153 1OPB RET 0.002411 0.43437 9.70149
154 4QYN RTL 0.001096 0.44209 9.77444
155 2AGC DAO 0.003496 0.45648 9.93377
156 4AZT LY2 0.008806 0.43119 9.93377
157 5XLY C2E 0.01128 0.41085 9.93377
158 1H8S AIC 0.02631 0.41078 9.93377
159 1GP6 DH2 0.005544 0.40614 9.93377
160 1GP6 SIN 0.005544 0.40614 9.93377
161 1GP6 QUE 0.006436 0.40077 9.93377
162 4WVW SLT 0.008989 0.41569 10.4167
163 1A78 TDG 0.003262 0.45983 10.4478
164 1GT4 UNA 0.002333 0.44672 10.596
165 5GLT BGC GAL NAG GAL 0.01224 0.42186 10.596
166 1NX0 ALA LYS ALA ILE ALA 0.03372 0.41616 10.596
167 2YAB AMP 0.01239 0.40574 10.596
168 4D4U FUC GAL NAG 0.04996 0.40007 10.596
169 3NNT DQA 0.03587 0.40003 10.596
170 4H2X G5A 0.00248 0.43751 10.6796
171 1LFO OLA 0.01327 0.40439 11.7188
172 5X7Q GLC GLC GLC GLC GLC 0.0004556 0.51496 11.9205
173 5X7Q GLC GLC GLC GLC 0.0004805 0.512 11.9205
174 1DZT TPE 0.02717 0.41279 11.9205
175 5KJW 53C 0.01014 0.43878 12.5828
176 4N14 WR7 0.01976 0.42549 12.5828
177 1GQG DCD 0.01179 0.40071 12.5828
178 1QY1 PRZ 0.001068 0.44625 13.245
179 2YKL NLD 0.004479 0.44158 13.245
180 1I06 TZL 0.01594 0.42657 13.245
181 2R5V HHH 0.01859 0.41088 13.245
182 4YZ5 SLT 0.004985 0.45638 13.9073
183 4OCT AKG 0.003123 0.45403 13.9073
184 1UMZ BGC BGC XYS BGC XYS GAL 0.01419 0.42482 13.9073
185 2ZHL NAG GAL GAL NAG 0.01071 0.4228 14.1892
186 4H2V AMP 0.005196 0.41627 14.5455
187 3PUR 2HG 0.01832 0.4262 14.5695
188 5JZJ AN2 0.0162 0.40679 14.5695
189 4P7X AKG 0.00126 0.45501 15.2318
190 4P7X YCP 0.00126 0.45501 15.2318
191 2V73 SIA 0.009979 0.43093 15.2318
192 1S68 AMP 0.02863 0.4129 15.2318
193 5H9P TD2 0.01252 0.4322 15.894
194 1YKD CMP 0.0148 0.40536 15.894
195 2C49 ADN 0.003839 0.4326 16.5563
196 1OFL NGK GCD 0.0188 0.41064 17.2185
197 4Q5H ANP 0.003449 0.43475 18.4211
198 4YLZ LAT NAG GAL 0.0003647 0.51742 18.543
199 4YGF AZM 0.01148 0.40726 19.2053
200 1PVC ILE SER GLU VAL 0.01426 0.4395 22.5166
201 1MEX RAC 0.01447 0.42021 22.5166
202 1N5S ADL 0.009801 0.41717 23.2143
203 3M3E GAL A2G NPO 0.007357 0.44544 24.5033
204 5VNF VAL THR SER VAL VAL 0.02977 0.40795 24.5033
205 3AVR OGA 0.03503 0.40967 27.2727
206 4L4V 1VY 0.01426 0.40943 27.2727
207 2E56 MYR 0.00005646 0.46872 36.1111
208 1MDC PLM 0.006014 0.41044 37.1212
Pocket No.: 2; Query (leader) PDB : 3MTX; Ligand: PGT; Similar sites found: 53
This union binding pocket(no: 2) in the query (biounit: 3mtx.bio2) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3ZW2 GLA NAG GAL FUC 0.01468 0.41003 None
2 3ZO7 K6H 0.03874 0.40614 None
3 1QIN GIP 0.00314 0.40522 None
4 4BJ8 BTN 0.02358 0.40336 None
5 2ARC ARA 0.04874 0.40078 None
6 1R5L VIV 0.008115 0.40398 1.3245
7 2QX0 PH2 0.02238 0.4234 2.64901
8 4D06 NAR 0.008237 0.4122 2.64901
9 4BIX ADP 0.03567 0.41198 2.64901
10 2QZ3 XYP XYP XYP 0.01057 0.40738 2.64901
11 1ZP9 ATP 0.02889 0.40225 2.64901
12 1O6U PLM 0.01824 0.40877 3.97351
13 1U6R ADP 0.007652 0.42339 4.63576
14 3OFM 4B0 0.03318 0.40255 4.63576
15 5H9Y BGC BGC BGC BGC 0.02923 0.402 4.63576
16 3B6R ADP 0.005926 0.43231 5.29801
17 5L6G XYP 0.01836 0.41005 5.29801
18 1ND2 MYR 0.003801 0.44568 5.96026
19 1IND EOT 0.02264 0.42839 5.96026
20 4EKQ NPO 0.01613 0.42228 5.96026
21 1T36 ORN 0.04927 0.40426 5.96026
22 5LY1 PPI 0.01263 0.40265 5.96026
23 1BHX ASP PHE GLU GLU ILE 0.0309 0.40764 6.12245
24 3UB7 ACM 0.04485 0.40634 6.62252
25 2P7Q GG6 0.01351 0.43046 6.76692
26 1WBI BTN 0.01789 0.41257 6.97674
27 2HRL SIA GAL SIA BGC NGA CEQ 0.04558 0.40235 7.08661
28 3P5P A3C 0.01615 0.40201 7.28477
29 1EPB REA 0.02551 0.40171 7.28477
30 5KBF CMP 0.008142 0.42943 8.60927
31 5K8S CMP 0.01797 0.40587 8.78378
32 1WW5 SGA BGC 0.01572 0.43367 9.27152
33 4C2C ALA ALA ALA 0.03145 0.42031 9.27152
34 4CJN QNZ 0.0465 0.40819 9.27152
35 1X14 NAD 0.01764 0.40625 9.27152
36 4D4U FUC GAL NDG FUC 0.02284 0.41447 10.596
37 5AIG VPR 0.02101 0.41634 11.2
38 5ML3 DL3 0.001893 0.4007 12.0805
39 3DAK ANP 0.01092 0.42316 12.5828
40 3C0G 3AM 0.03575 0.40089 12.5828
41 3EWK FAD 0.01826 0.40249 13.245
42 2QL9 CIT 0.009126 0.44164 13.4021
43 3SLS 77D 0.01472 0.40997 13.9073
44 3N9P OGA 0.03648 0.41126 14.5695
45 3A23 GAL 0.03899 0.40986 14.5695
46 3N9O OGA 0.04531 0.40532 14.5695
47 3N9Q OGA 0.04713 0.40415 14.5695
48 4CLO XP0 0.03409 0.40887 17.2185
49 4C2W ANP 0.02799 0.40988 17.3077
50 4KBA 1QM 0.02682 0.41467 17.8808
51 3B00 16A 0.03236 0.4031 20.5298
52 2JIG PD2 0.04616 0.40205 21.1921
53 1DMY AZM 0.0134 0.42644 23.8411
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