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 28 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 25 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 24 families.
1 2IU8 - PLM C16 H32 O2 CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLM; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 F23 1 1
3 11A 1 1
4 STE 1 1
5 KNA 1 1
6 TDA 1 1
7 DCR 1 1
8 DAO 1 1
9 DKA 1 1
10 PLM 1 1
11 F15 1 1
12 OCA 0.956522 1
13 SHV 0.833333 0.952381
14 KTC 0.793103 0.875
15 AZ1 0.73913 0.64
16 6NA 0.72 0.904762
17 NER 0.71875 0.954545
18 OLA 0.71875 0.954545
19 ELA 0.71875 0.954545
20 VCA 0.666667 0.954545
21 PAM 0.666667 0.954545
22 PML 0.625 0.6
23 3LA 0.606061 0.8
24 LEA 0.6 0.809524
25 MYZ 0.588235 0.909091
26 12H 0.586207 0.615385
27 ODD 0.567568 0.913043
28 BRC 0.566667 0.666667
29 14V 0.555556 0.740741
30 M12 0.545455 0.869565
31 14U 0.542857 0.703704
32 EIC 0.538462 0.913043
33 EOD 0.538462 0.7
34 BUA 0.48 0.666667
35 RCL 0.468085 0.84
36 HXD 0.459459 0.807692
37 56S 0.459459 0.653846
38 ODT 0.452381 0.782609
39 3X1 0.444444 0.818182
40 LNL 0.44186 0.826087
41 CNS 0.435897 0.68
42 6UL 0.435897 0.68
43 5UF 0.432432 0.807692
44 243 0.428571 0.807692
45 GYM 0.418605 0.606061
46 PL3 0.413793 0.75
47 O8N 0.413793 0.75
48 1DO 0.413793 0.75
49 F09 0.413793 0.75
50 OC9 0.413793 0.75
51 DE1 0.413793 0.75
52 T25 0.403846 0.677419
Ligand no: 2; Ligand: UD1; Similar ligands found: 76
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 EEB 0.742857 0.971429
7 EPU 0.742857 0.971429
8 UD4 0.742574 0.957143
9 UPG 0.73913 0.985294
10 UFM 0.73913 0.985294
11 GUD 0.73913 0.985294
12 GDU 0.73913 0.985294
13 UD7 0.722772 0.971014
14 MJZ 0.715686 0.957143
15 U2F 0.697917 0.930556
16 UPF 0.697917 0.930556
17 UMA 0.690265 0.985507
18 UDM 0.683168 0.957143
19 UFG 0.663265 0.930556
20 HWU 0.660377 0.943662
21 12V 0.660377 0.943662
22 U22 0.655462 0.85
23 U21 0.655462 0.871795
24 U20 0.655462 0.871795
25 UGA 0.65 0.970588
26 UGB 0.65 0.970588
27 USQ 0.633663 0.835443
28 UAD 0.63 0.956522
29 UDX 0.63 0.956522
30 UDP 0.622222 0.927536
31 UTP 0.619565 0.927536
32 UAG 0.617188 0.931507
33 URM 0.6 0.942857
34 660 0.6 0.942857
35 G3N 0.596154 0.929577
36 UPU 0.587629 0.955882
37 4RA 0.584615 0.87013
38 UNP 0.583333 0.901408
39 3UC 0.575472 0.930556
40 UML 0.564286 0.871795
41 IUG 0.561404 0.825
42 U5P 0.555556 0.913043
43 UDP GAL 0.552381 0.956522
44 UD0 0.552239 0.858974
45 UDH 0.543689 0.855263
46 UPP 0.543689 0.928571
47 2KH 0.530612 0.901408
48 44P 0.521277 0.888889
49 C5G 0.518519 0.930556
50 UDP UDP 0.505155 0.898551
51 Y6W 0.504673 0.90411
52 2QR 0.485075 0.860759
53 2GW 0.482759 0.943662
54 U 0.477273 0.852941
55 URI 0.477273 0.852941
56 UP5 0.47541 0.844156
57 1GW 0.467213 0.905405
58 CJB 0.461538 0.838235
59 PMP UD1 0.460432 0.833333
60 4TC 0.456 0.822785
61 UAG API 0.453947 0.881579
62 CSV 0.452991 0.866667
63 CSQ 0.452991 0.866667
64 UA3 0.447917 0.898551
65 U3P 0.447917 0.898551
66 U U 0.446429 0.914286
67 GN1 0.444444 0.753623
68 NG1 0.444444 0.753623
69 PUP 0.429825 0.875
70 CXY 0.422414 0.90411
71 A U 0.418605 0.820513
72 U2P 0.418367 0.913043
73 UMA FGA LYS DAL DAL 0.417178 0.858974
74 U1S 0.409091 0.789474
75 FN5 0.40458 0.883117
76 DAU 0.403361 0.905405
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2IU8; Ligand: PLM; Similar sites found: 58
This union binding pocket(no: 1) in the query (biounit: 2iu8.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4I3V NAD 0.00651 0.41199 1.60428
2 3HAZ NAD 0.001899 0.43398 1.87166
3 2POC UD1 0.0001431 0.41574 1.90736
4 3ZJX BOG 0.02129 0.40888 2.07612
5 1LVL FAD 0.04922 0.40887 2.13904
6 2C78 PUL 0.02673 0.40428 2.40642
7 4XTX 590 0.002408 0.42949 2.59259
8 1I0Z NAI 0.009605 0.40335 2.7027
9 1LSH PLD 0.001578 0.43604 2.94118
10 3JZ4 NAP 0.001094 0.40285 2.94118
11 1HXD BTN 0.002075 0.41554 3.42679
12 4DQ2 BTX 0.0008743 0.44712 3.65854
13 2WOX NDP 0.0043 0.42357 3.74332
14 1KY8 NAP 0.007312 0.42066 3.74332
15 4MDB RLT 0.01273 0.41147 4
16 4GID 0GH 0.01143 0.44148 4.27807
17 3KYG 5GP 5GP 0.003193 0.40298 4.40529
18 1BW9 PPY 0.01219 0.40346 4.49438
19 1C1X HFA 0.01156 0.40833 4.50704
20 3VZ3 NAP 0.009643 0.40453 5.08021
21 3L9R L9Q 0.01112 0.40417 5.10204
22 4LH0 GLV 0.006363 0.41828 5.61497
23 3NCQ ATP 0.002069 0.41948 5.88235
24 3EFS BTN 0.001322 0.4192 6.00858
25 4IEN GDP 0.001885 0.40184 6.13497
26 3ITJ FAD 0.0195 0.40709 6.21302
27 4PZ2 NAD 0.002142 0.43307 6.41711
28 3HVJ 705 0.01544 0.40211 6.78733
29 1V3S ATP 0.001097 0.42717 6.89655
30 3FSY SCA 0.003221 0.4182 6.92771
31 4LSJ LSJ 0.02061 0.40361 7.36434
32 3LF0 ATP 0.002423 0.41843 7.89474
33 4CS4 AXZ 0.01297 0.41116 8.39416
34 4CS4 ANP 0.01081 0.40905 8.39416
35 2J9C ATP 0.003381 0.4173 8.40336
36 2J9D ADP 0.00401 0.40748 8.40336
37 1WPY BTN 0.003929 0.41602 8.51064
38 1T90 NAD 0.001796 0.43641 8.55615
39 1O9J NAD 0.001617 0.43701 9.09091
40 2DXU BT5 0.00311 0.42601 9.3617
41 5JCA NDP 0.0377 0.40099 9.62567
42 3TAY MN0 0.003244 0.41648 9.81595
43 5L2J 6UL 0.008244 0.43311 10.2041
44 5L2J 70E 0.00877 0.43311 10.2041
45 2J4K U5P 0.006045 0.41927 11.0619
46 1TT8 PHB 0.001845 0.42852 12.1951
47 2IMP NAI 0.00992 0.40968 12.5668
48 2WLG SOP 0.003427 0.44369 13.9535
49 4USI ATP 0.001016 0.43235 15.5844
50 3VBK COA 0.002546 0.44139 16.0976
51 3VBK 0FX 0.003008 0.44103 16.0976
52 4Q3F TLA 0.02888 0.40494 18.8034
53 2VBU CDP 0.01263 0.40057 19.1176
54 5DEP UD1 0.00006622 0.51044 31.3953
55 3I3X U22 0.00001133 0.54341 32.8185
56 5N2F 8HW 0.001266 0.43026 33.3333
57 5N2D 8J8 0.00218 0.41108 34.7222
58 2QIA U20 0.00003773 0.5143 36.6412
Pocket No.: 2; Query (leader) PDB : 2IU8; Ligand: UD1; Similar sites found: 10
This union binding pocket(no: 2) in the query (biounit: 2iu8.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1RM0 NAI 0.02243 0.41042 1.06952
2 2GN3 MMA 0.01953 0.41014 2.77778
3 2GN3 MAN 0.02046 0.40931 2.77778
4 2ZJ1 ARJ 0.03755 0.40312 2.94118
5 2ZJ1 NAD 0.04033 0.40157 2.94118
6 1COY AND 0.03807 0.40618 7.21925
7 1COY FAD 0.02485 0.40488 7.21925
8 4R33 SAH 0.007166 0.42244 8.82353
9 4R33 TRP 0.007166 0.42244 8.82353
10 3I3X U22 0.01404 0.41401 32.8185
Pocket No.: 3; Query (leader) PDB : 2IU8; Ligand: PLM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2iu8.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2IU8; Ligand: PLM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2iu8.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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