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Receptor
PDB id Resolution Class Description Source Keywords
2IU8 2.2 Å EC: 2.3.1.- CHLAMYDIA TRACHOMATIS LPXD WITH 25MM UDPGLCNAC (COMPLEX I) CHLAMYDIA TRACHOMATIS TRANSFERASE UDP-3- O-ACYL-GLUCOSAMINE N-ACYLTRANSFERASE ACYLTRANSFERASE LIPID A BIOSYNTHESIS LEFT-HANDED BETA HELIX COMPLEX WITH UDPGLCNAC ENZYME HOMOTRIMER LIPID SYNTHESIS
Ref.: STRUCTURE AND REACTIVITY OF LPXD, THE N-ACYLTRANSFERASE OF LIPID A BIOSYNTHESIS PROC.NATL.ACAD.SCI.USA V. 104 4321 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BME A:1351;
 Invalid;
 none;
 submit data
78.133 C2 H6 O S C(CS)...
EDO A:1350;
 Invalid;
 none;
 submit data
62.068 C2 H6 O2 C(CO)...
PLM A:1349;
B:1349;
C:1351;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
256.424 C16 H32 O2 CCCCC...
SO4 A:1347;
A:1348;
B:1346;
B:1347;
C:1349;
C:1350;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
UD1 B:1348;
 Valid;
 none;
 submit data
607.354 C17 H27 N3 O17 P2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2IU8 2.2 Å EC: 2.3.1.- CHLAMYDIA TRACHOMATIS LPXD WITH 25MM UDPGLCNAC (COMPLEX I) CHLAMYDIA TRACHOMATIS TRANSFERASE UDP-3- O-ACYL-GLUCOSAMINE N-ACYLTRANSFERASE ACYLTRANSFERASE LIPID A BIOSYNTHESIS LEFT-HANDED BETA HELIX COMPLEX WITH UDPGLCNAC ENZYME HOMOTRIMER LIPID SYNTHESIS
Ref.: STRUCTURE AND REACTIVITY OF LPXD, THE N-ACYLTRANSFERASE OF LIPID A BIOSYNTHESIS PROC.NATL.ACAD.SCI.USA V. 104 4321 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 33 families.
1 2IU8 - PLM C16 H32 O2 CCCCCCCCCC....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 30 families.
1 2IU8 - PLM C16 H32 O2 CCCCCCCCCC....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 2IU8 - PLM C16 H32 O2 CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLM; 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
Ligand no: 2; Ligand: UD1; Similar ligands found: 79
No: Ligand ECFP6 Tc MDL keys Tc
1 UD2 1 1
2 UD1 1 1
3 UDZ 0.8 0.893333
4 HP7 0.793814 0.985294
5 EPZ 0.75 0.985507
6 EPU 0.742857 0.971429
7 EEB 0.742857 0.971429
8 F5P 0.742574 0.957143
9 UD4 0.742574 0.957143
10 F5G 0.742574 0.971014
11 UFM 0.73913 0.985294
12 GUD 0.73913 0.985294
13 UPG 0.73913 0.985294
14 GDU 0.73913 0.985294
15 UD7 0.722772 0.971014
16 MJZ 0.715686 0.957143
17 U2F 0.697917 0.930556
18 UPF 0.697917 0.930556
19 UMA 0.690265 0.985507
20 UDM 0.683168 0.957143
21 UFG 0.663265 0.930556
22 12V 0.660377 0.943662
23 HWU 0.660377 0.943662
24 U22 0.655462 0.85
25 U20 0.655462 0.871795
26 U21 0.655462 0.871795
27 UGB 0.65 0.970588
28 UGA 0.65 0.970588
29 USQ 0.633663 0.835443
30 UDX 0.63 0.956522
31 UAD 0.63 0.956522
32 UDP 0.622222 0.927536
33 UTP 0.619565 0.927536
34 UAG 0.617188 0.931507
35 660 0.6 0.942857
36 URM 0.6 0.942857
37 G3N 0.596154 0.929577
38 UPU 0.587629 0.955882
39 4RA 0.584615 0.87013
40 UNP 0.583333 0.901408
41 3UC 0.575472 0.930556
42 UML 0.564286 0.871795
43 IUG 0.561404 0.825
44 U5P 0.555556 0.913043
45 U 0.555556 0.913043
46 UD0 0.552239 0.858974
47 UPP 0.543689 0.928571
48 UDH 0.543689 0.855263
49 2KH 0.530612 0.901408
50 44P 0.521277 0.888889
51 C5G 0.518519 0.930556
52 UDP UDP 0.505155 0.898551
53 Y6W 0.504673 0.90411
54 2QR 0.485075 0.860759
55 2GW 0.482759 0.943662
56 URI 0.477273 0.852941
57 UP5 0.47541 0.844156
58 PMP UD1 0.467626 0.848101
59 1GW 0.467213 0.905405
60 CJB 0.461538 0.838235
61 UAG API 0.457516 0.87013
62 4TC 0.456 0.822785
63 CSV 0.452991 0.866667
64 CSQ 0.452991 0.866667
65 U3P 0.447917 0.898551
66 UA3 0.447917 0.898551
67 U U 0.446429 0.914286
68 NG1 0.444444 0.753623
69 GN1 0.444444 0.753623
70 C30 0.433628 0.696203
71 PUP 0.429825 0.875
72 CXY 0.422414 0.90411
73 A U 0.418605 0.820513
74 U2P 0.418367 0.913043
75 UMA FGA LYS DAL DAL 0.414634 0.8375
76 U1S 0.409091 0.789474
77 FN5 0.40458 0.883117
78 DAU 0.403361 0.905405
79 G U 0.401515 0.780488
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2IU8; Ligand: PLM; Similar sites found with APoc: 180
This union binding pocket(no: 1) in the query (biounit: 2iu8.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5CLO NS8 None
2 5O3Q CMP None
3 5XH2 NPO 1.14504
4 5KJW 53C 1.3369
5 4I3V NAD 1.60428
6 6F5W KG1 1.62602
7 3ACL 3F1 1.68919
8 3HAZ NAD 1.87166
9 6E1Q CFA 1.87166
10 2POC UD1 1.90736
11 4L80 OXL 2.01149
12 3ZJX BOG 2.07612
13 6APL C5P 2.13904
14 3IWJ NAD 2.13904
15 1Q11 TYE 2.15054
16 6GNO XDI 2.22222
17 2I7N ACO 2.22222
18 5N5S NAP 2.3301
19 5AHN IMP 2.40642
20 5OD2 5ID 2.40642
21 4XFM THE 2.40642
22 2C78 PUL 2.40642
23 5H9I XAN 2.5
24 5N5U 7N8 2.54777
25 4XTX 590 2.59259
26 1OFL NGK GCD 2.6738
27 5D9G GLU ASN LEU TYR PHE GLN 2.84553
28 1LSH PLD 2.94118
29 3JZ4 NAP 2.94118
30 5A1S FLC 2.94118
31 6EWZ APC 2.95359
32 3SAO DBH 3.125
33 6B5G NAD 3.20856
34 1GPM AMP 3.20856
35 4RD0 GDP 3.20856
36 6B5G CQY 3.20856
37 3RHJ NAP 3.20856
38 2IVD ACJ 3.20856
39 4JF5 FLC 3.29218
40 6CAM BGC 3.38983
41 2CYB TYR 3.40557
42 1HXD BTN 3.42679
43 4NZ6 DGL 3.51438
44 5YRG BGC GLC 3.52113
45 5YRJ BGC GLC 3.52113
46 6BYF CIT 3.52941
47 4DQ2 BTX 3.65854
48 3A3B RBF 3.68421
49 1UTJ ABN 3.71901
50 4A0M NAD 3.74332
51 1KY8 NAP 3.74332
52 2WOX NDP 3.74332
53 2WME NAP 3.74332
54 1YRO UDP 3.84615
55 4MDB RLT 4
56 5L13 6ZE 4.01069
57 3NKS ACJ 4.01069
58 5YJS SAL 4.01069
59 4RF7 ARG 4.01069
60 5FQD LVY 4.01069
61 1OSS BEN 4.03587
62 5DYO FLU 4.12844
63 5MUA GAL 4.1958
64 5OCG 9R5 4.2328
65 5MRH Q9Z 4.27807
66 3DOO SKM 4.33213
67 3KYG 5GP 5GP 4.40529
68 1TVP CBI 4.43686
69 4RT1 C2E 4.46429
70 1BXG HCI 4.49438
71 1BW9 PPY 4.49438
72 1C1X HFA 4.50704
73 5LUN OGA 4.54545
74 5J75 6GQ 4.54545
75 2EV9 SKM 4.56274
76 6FA4 D1W 4.62428
77 5TCI MLI 4.71014
78 3TCT 3MI 4.72441
79 4PXL NAD 4.81283
80 2Y5D NAP 4.81283
81 3QSB 743 4.91803
82 2AGC DAO 4.93827
83 6B3V ANP 5.08021
84 6B3V 7DQ 5.08021
85 5CQG 55C 5.08021
86 3VZ3 NAP 5.08021
87 3L9R L9Q 5.10204
88 3KYF 5GP 5GP 5.19481
89 6FK3 PPI 5.34759
90 3A75 GLU 5.34759
91 1SDW IYT 5.41401
92 2VL1 GLY GLY 5.61497
93 4LH0 GLV 5.61497
94 5TUF TDC 5.61497
95 3KIF GDL 5.66038
96 4FBL SPD 5.69395
97 5F6U 5VK 5.73248
98 2CJU PHX 5.78512
99 1G51 AMP 5.88235
100 3NCQ ATP 5.88235
101 4WCX MET 5.88235
102 3EFS BTN 6.00858
103 3C3N FMN 6.08974
104 4IEN GDP 6.13497
105 2BJK NAD 6.14973
106 4CJN QNZ 6.14973
107 5Y4R C2E 6.2069
108 3ITJ FAD 6.21302
109 4PZ2 NAD 6.41711
110 4Z87 GDP 6.41711
111 2PNC CLU 6.41711
112 3HVJ 705 6.78733
113 1V3S ATP 6.89655
114 3FSY SCA 6.92771
115 3QXV MTX 7.14286
116 2OMN IPH 7.37327
117 5G48 1FL 7.48663
118 1F9V ADP 7.4928
119 5O74 GDP 7.61421
120 6G47 SIA 7.6555
121 4RYV ZEA 7.74194
122 3LF0 ATP 7.89474
123 2G30 ALA ALA PHE 8.13953
124 5AZC PGT 8.33333
125 1W55 C 8.35579
126 4CS4 AXZ 8.39416
127 4CS4 ANP 8.39416
128 2J9D ADP 8.40336
129 2J9C ATP 8.40336
130 3LL5 IP8 8.43373
131 1WPY BTN 8.51064
132 1T90 NAD 8.55615
133 2HK9 SKM 8.72727
134 3PCJ INO 8.82353
135 5H9P TD2 8.86076
136 1O9J NAD 9.09091
137 2DXU BT5 9.3617
138 2RDE C2E 9.56175
139 2H6B 3C4 9.6
140 2O07 MTA 9.62567
141 2O07 SPD 9.62567
142 5JCA NDP 9.62567
143 4FE2 AIR 9.80392
144 5OM2 DXT 10.0271
145 5WL1 D3D 10.101
146 5WL1 CUY 10.101
147 4MOB ADP 10.241
148 3QPB URA 10.2837
149 4TQK NAG 10.4278
150 5L2R MLA 10.9626
151 2J4K U5P 11.0619
152 3RF4 FUN 11.2069
153 1I7M CG 11.9403
154 3DZ6 M8E 11.9403
155 1NX0 ALA LYS ALA ILE ALA 12.1387
156 1TT8 PHB 12.1951
157 2V7Y ADP 12.2995
158 2IMP NAI 12.5668
159 4L50 D8X 12.782
160 2WLG SOP 13.9535
161 3GXZ NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 14.8515
162 4USI ATP 15.5844
163 4F8L GAL 15.8621
164 3VBK COA 16.0976
165 3VBK 0FX 16.0976
166 5EJL C2E 16.9355
167 5TVF CGQ 17.6471
168 1GG6 APL 18.3206
169 6C5F 7L9 18.8034
170 2VBU CDP 19.1176
171 1WAP TRP 20
172 3IWD M2T 20.9677
173 3TWD GOB 28.8288
174 5DEP UD1 31.3953
175 3I3X U22 32.8185
176 1J2Z SOG 33.3333
177 5N2F 8HW 33.3333
178 5N2D 8J8 34.7222
179 5FUI APY 36.3636
180 2QIA U20 36.6412
Pocket No.: 2; Query (leader) PDB : 2IU8; Ligand: UD1; Similar sites found with APoc: 23
This union binding pocket(no: 2) in the query (biounit: 2iu8.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1RM0 NAI 1.06952
2 2POC BG6 1.90736
3 4UP4 GAL NAG 2.40642
4 6BND OPE 2.61628
5 1WOG 16D 2.62295
6 2GN3 MMA 2.77778
7 2GN3 MAN 2.77778
8 2GNB MAN 2.77778
9 2ZJ1 ARJ 2.94118
10 5YS9 FAD 2.94118
11 1PIG GLC GLC 2.94118
12 2ZJ1 NAD 2.94118
13 5X7Q GLC GLC GLC GLC 3.20856
14 5X7Q GLC GLC GLC GLC GLC 3.20856
15 5MB4 NAG 3.47594
16 5DOZ NDP 3.5503
17 6HTO 5AD 6.25
18 6HTO MET 6.25
19 4M1U A2G MBG 7.14286
20 1COY AND 7.21925
21 1COY FAD 7.21925
22 3O5N BR0 8.03571
23 4LO6 SIA GAL 9.47368
Pocket No.: 3; Query (leader) PDB : 2IU8; Ligand: PLM; Similar sites found with APoc: 76
This union binding pocket(no: 3) in the query (biounit: 2iu8.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5HWV MBN None
2 1RYD GLC 1.3369
3 4ZUL UN1 1.60428
4 2Z48 NGA 1.87166
5 4OE4 NAD 1.87166
6 5UCD NAP 2.13904
7 3OQJ 3CX 2.33463
8 5IUW NAD 2.40642
9 4UP4 GAL NAG 2.40642
10 5IUW IAC 2.40642
11 6CEP NAD 2.69461
12 6CEP OXM 2.69461
13 9LDT NAD 2.71084
14 1C5C TK4 2.80374
15 2JLD AG1 2.94118
16 5XDT ZI7 2.94118
17 5E3Q SCA 2.98013
18 4XW2 SIM 3.0303
19 1GS5 NLG 3.10078
20 1GS5 ANP 3.10078
21 5KF6 NAD 3.47594
22 2NU8 COA 3.47594
23 3VSV XYS 3.47594
24 1QO8 FAD 3.47594
25 4GK9 MAN BMA MAN MAN MAN 3.58423
26 3A3B FMN 3.68421
27 3NZ1 3NY 3.83142
28 2E1A MSE 4
29 2QE0 NAP 4.01069
30 3FIU AMP 4.01606
31 4TS1 TYR 4.07523
32 5A89 FMN 4.48718
33 1C1D PHE 4.50704
34 4I8P NAD 4.54545
35 3TW1 AHN 5.06329
36 1Q9I TEO 5.08021
37 1Q9I FAD 5.08021
38 3VZ3 SSN 5.08021
39 6AMI TRP 5.08021
40 5GUD NDP 5.08021
41 3RNM FAD 5.17241
42 1UYY BGC BGC 5.34351
43 5TUF FAD 5.61497
44 3HRD NIO 5.625
45 5L2M 6ZY 5.88235
46 4ZSD 7I6 6.14973
47 4M52 M52 6.14973
48 2J5B TYE 6.32184
49 4YLZ LAT NAG GAL 6.53595
50 4L3L 5FI 6.57895
51 2HJ4 PNZ 6.66667
52 4WOE ADP 6.68449
53 5XLY C2E 6.76692
54 5HTX ADP 6.95187
55 3PNQ 2HA 7.0028
56 1NFU RRP 7.87402
57 5UKL SIX 8.06452
58 2XG5 EC5 8.67052
59 2XG5 EC2 8.67052
60 4NTO 1PW 9.17874
61 3ZZQ TRP 9.23077
62 3TAY MN0 9.81595
63 3EM0 CHD 10.1449
64 1KGI T4A 10.2362
65 3ZF8 GDP 10.4918
66 43CA NPO 11.5044
67 1QAW TRP 13.5135
68 1KRR ACO 14.2857
69 3S5W NAP 14.7059
70 3ZZS TRP 15.3846
71 1T3D CYS 15.917
72 1HV9 COA 16.5775
73 4CQM NAP 17.2414
74 3BP1 GUN 17.2414
75 4MZU COA 23.0769
76 5NIU 8YZ 32.8125
Pocket No.: 4; Query (leader) PDB : 2IU8; Ligand: PLM; Similar sites found with APoc: 47
This union binding pocket(no: 4) in the query (biounit: 2iu8.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5AOG IAC 1.62866
2 1H3F TYE 1.87166
3 1IT7 GUN 1.87166
4 6MVU K4V 2.13904
5 5C9P FUC 2.40642
6 3AI3 SOE 2.6616
7 4OYA 1VE 2.94118
8 2Z3U CRR 3.20856
9 2V2G BEZ 3.43348
10 4YDU ADP 3.47594
11 3RSJ NGA GAL SIA 3.74332
12 1D4D FAD 3.84615
13 3DLG GWE 4.01069
14 3BJE R1P 4.01146
15 2CYC TYR 4.27807
16 3EYA TDP 4.27807
17 4I9B NAD 4.54545
18 2YVJ NAI 4.58716
19 3KCC CMP 4.61538
20 1A5Z FBP 4.70219
21 6ER9 FAD 4.81283
22 6ER9 NAP 4.81283
23 1R6B ADP 5.34759
24 1LDN NAD 5.37975
25 1KNM LAT 5.38462
26 2V5K OXM 5.57491
27 4G9N NGA 5.59441
28 2A8X FAD 5.61497
29 2RCU BUJ 6.14973
30 5X5U NAD 6.14973
31 3LE7 ADE 6.51341
32 2GPT SKM 6.68449
33 2VWT PYR 6.74157
34 5LXT GTP 6.99301
35 4K55 H6P 7.25806
36 1SJD NPG 7.88043
37 2J9D AMP 8.40336
38 1WD4 AHR 8.55615
39 3KU0 ADE 9.96016
40 3CBC DBS 10.101
41 2PT9 2MH 10.2804
42 3QPB R1P 10.2837
43 1GXS BEZ 10.7595
44 2GAG FOA 11.9048
45 2GAG NAD 11.9048
46 2GOO NDG 13.7405
47 2Y7P SAL 15.1376
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