Receptor
PDB id Resolution Class Description Source Keywords
4PQG 2 Å EC: 2.4.1.- CRYSTAL STRUCTURE OF THE PNEUMOCOCCAL O-GLCNAC TRANSFERASE G COMPLEX WITH UDP AND GLCNAC STREPTOCOCCUS PNEUMONIAE O-GLCNAC TRANSFERASE GT-B FOLD ROSSMANN FOLD GTFB TRANSF
Ref.: STRUCTURE OF A NOVEL O-LINKED N-ACETYL-D-GLUCOSAMIN (O-GLCNAC) TRANSFERASE, GTFA, REVEALS INSIGHTS INTO GLYCOSYLATION OF PNEUMOCOCCAL SERINE-RICH REPEAT AD J.BIOL.CHEM. V. 289 20898 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UDP B:601;
A:601;
Valid;
Valid;
none;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
NAG A:602;
B:602;
Valid;
Valid;
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
4PQG 2 Å EC: 2.4.1.- CRYSTAL STRUCTURE OF THE PNEUMOCOCCAL O-GLCNAC TRANSFERASE G COMPLEX WITH UDP AND GLCNAC STREPTOCOCCUS PNEUMONIAE O-GLCNAC TRANSFERASE GT-B FOLD ROSSMANN FOLD GTFB TRANSF
Ref.: STRUCTURE OF A NOVEL O-LINKED N-ACETYL-D-GLUCOSAMIN (O-GLCNAC) TRANSFERASE, GTFA, REVEALS INSIGHTS INTO GLYCOSYLATION OF PNEUMOCOCCAL SERINE-RICH REPEAT AD J.BIOL.CHEM. V. 289 20898 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 4PQG - NAG C8 H15 N O6 CC(=O)N[C@....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 4PQG - NAG C8 H15 N O6 CC(=O)N[C@....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 4PQG - NAG C8 H15 N O6 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UDP; Similar ligands found: 116
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 UNP 0.8 0.970149
4 U5P 0.78125 0.984615
5 UPU 0.72973 0.940298
6 2KH 0.722222 0.970149
7 44P 0.720588 0.955882
8 URM 0.717949 0.927536
9 GUD 0.717949 0.941176
10 GDU 0.717949 0.941176
11 UFM 0.717949 0.941176
12 UPG 0.717949 0.941176
13 660 0.717949 0.927536
14 UDP UDP 0.714286 0.939394
15 UDH 0.705128 0.864865
16 UPP 0.705128 0.941176
17 UPF 0.691358 0.888889
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UDX 0.670732 0.941176
21 UAD 0.670732 0.941176
22 3UC 0.658824 0.888889
23 USQ 0.654762 0.820513
24 UGB 0.654762 0.955224
25 UGA 0.654762 0.955224
26 G3N 0.647059 0.914286
27 UDM 0.636364 0.914286
28 URI 0.625 0.863636
29 U 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 UDP GAL 0.611765 0.913043
33 Y6W 0.607143 0.888889
34 CDP 0.605263 0.942029
35 UD7 0.591398 0.927536
36 HP7 0.591398 0.941176
37 MJZ 0.585106 0.914286
38 IUG 0.583333 0.810127
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 UD4 0.578947 0.914286
42 CJB 0.573529 0.820895
43 UDZ 0.571429 0.853333
44 DUD 0.571429 0.913043
45 UP5 0.571429 0.853333
46 U U 0.563218 0.955224
47 EPZ 0.56 0.914286
48 5GW 0.559524 0.942029
49 EPU 0.554455 0.901408
50 EEB 0.554455 0.901408
51 UA3 0.547945 0.939394
52 U3P 0.547945 0.939394
53 CH 0.546667 0.913043
54 4TC 0.544554 0.831169
55 CTP 0.54321 0.942029
56 CSV 0.531915 0.851351
57 CSQ 0.531915 0.851351
58 DUT 0.52439 0.913043
59 4GW 0.516484 0.915493
60 UMA 0.513761 0.914286
61 U4S 0.513158 0.753425
62 U2P 0.506667 0.954545
63 U2S 0.5 0.767123
64 U3S 0.5 0.753425
65 PUP 0.48913 0.913043
66 U22 0.486957 0.790123
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 DKX 0.486486 0.746479
70 U1S 0.482759 0.75
71 A U 0.481132 0.805195
72 2QR 0.478632 0.822785
73 5FU 0.474359 0.914286
74 8OD 0.47191 0.851351
75 C5G 0.468085 0.888889
76 7XL 0.465909 0.888889
77 U U U U 0.461538 0.940298
78 UMF 0.461538 0.857143
79 G8D 0.460674 0.855263
80 UTP U U U 0.456522 0.895522
81 2TU 0.452055 0.774648
82 4RA 0.451613 0.855263
83 C2G 0.450549 0.901408
84 DU 0.45 0.898551
85 CAR 0.45 0.927536
86 C 0.45 0.927536
87 C5P 0.45 0.927536
88 UMP 0.45 0.898551
89 UAG 0.448 0.864865
90 CDC 0.446809 0.777778
91 UD0 0.444444 0.844156
92 5BU 0.444444 0.914286
93 N3E 0.440476 0.733333
94 UC5 0.440476 0.9
95 UUA 0.438356 0.772727
96 DUP 0.431818 0.887324
97 2GW 0.431373 0.901408
98 M7G 0.430108 0.780488
99 CNU 0.428571 0.927536
100 CDM 0.427083 0.842105
101 H6Y 0.425532 0.851351
102 16B 0.421687 0.888889
103 S5P 0.419753 0.915493
104 8GT 0.419355 0.855263
105 CXY 0.418367 0.888889
106 UPA 0.418182 0.842105
107 CDP MG 0.413793 0.849315
108 U2G 0.410714 0.822785
109 U A A U 0.409836 0.842105
110 UML 0.408759 0.810127
111 UP6 0.407407 0.871429
112 M7M 0.40625 0.771084
113 PMP UD1 0.404762 0.794872
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
Ligand no: 2; Ligand: NAG; Similar ligands found: 109
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG 1 1
2 HSQ 1 1
3 NGA 1 1
4 A2G 1 1
5 NDG 1 1
6 BM3 1 1
7 BGN 0.638298 0.888889
8 SIZ 0.630435 0.906977
9 YX1 0.625 0.65
10 GAL NGA A2G 0.614035 0.816327
11 STZ 0.612245 0.65
12 16G 0.591837 0.735849
13 BMX 0.591837 0.735849
14 4QY 0.591837 0.735849
15 SNG 0.5625 0.866667
16 NGS 0.54902 0.661017
17 NAG GDL 0.54386 0.833333
18 CBS 0.54386 0.833333
19 CBS CBS 0.54386 0.833333
20 NAG NDG 0.54386 0.833333
21 ASG 0.538462 0.661017
22 BG8 0.537037 0.906977
23 2F8 0.530612 0.909091
24 MAG 0.530612 0.909091
25 NLC 0.517857 0.888889
26 GAL NDG 0.517857 0.888889
27 NDG GAL 0.517857 0.888889
28 NAG A2G 0.517241 0.833333
29 4V5 0.517241 0.829787
30 NAG NGA 0.517241 0.833333
31 MAN NAG 0.508772 0.888889
32 4UZ 0.508475 0.808511
33 NDG NAG NAG 0.508197 0.816327
34 CTO 0.508197 0.816327
35 NAG NAG NDG 0.508197 0.816327
36 NAG NAG NAG NDG 0.508197 0.816327
37 NAG NAG NAG NAG NAG NAG NAG NAG 0.508197 0.816327
38 NDG NAG NAG NDG 0.508197 0.816327
39 NAG NAG NAG NAG 0.508197 0.816327
40 NAG NAG NAG 0.508197 0.816327
41 NAG NAG NAG NAG NDG NAG 0.508197 0.816327
42 NAG NAG NAG NAG NAG NAG 0.508197 0.816327
43 NDG NAG NAG NDG NAG 0.508197 0.816327
44 NDG NAG NAG NAG 0.508197 0.816327
45 NAG NAG NAG NAG NDG 0.508197 0.816327
46 NAG NAG NAG NAG NAG 0.508197 0.816327
47 NBG 0.5 0.951219
48 MQG 0.5 0.698113
49 A2G GAL 0.491228 0.888889
50 GAL A2G 0.491228 0.888889
51 GAL NGA 0.491228 0.888889
52 AMU 0.490909 0.930233
53 GN1 0.490566 0.754717
54 NG1 0.490566 0.754717
55 NDG NAG 0.47541 0.816327
56 NAG GAL 0.474576 0.888889
57 NGA GAL 0.474576 0.888889
58 NAG FUC 0.474576 0.866667
59 GAL NAG 0.474576 0.888889
60 NAG GAL NAG 0.455882 0.833333
61 FUC NAG 0.45 0.888889
62 3YW 0.448276 0.930233
63 GLA GAL NAG 0.446154 0.888889
64 MAN BMA NAG 0.446154 0.888889
65 NAG GAL GAL 0.446154 0.888889
66 FUL GAL NAG 0.426471 0.869565
67 G6S NAG 0.426471 0.677966
68 DR2 0.426471 0.869565
69 FUC GAL NDG 0.426471 0.869565
70 FUC GAL NAG 0.426471 0.869565
71 NDG GAL FUC 0.426471 0.869565
72 GYU 0.42623 0.740741
73 TNR 0.42623 0.833333
74 NAG BDP 0.421875 0.851064
75 NAG MBG 0.419355 0.851064
76 NGA GAL BGC 0.41791 0.888889
77 NAG NAG 0.415385 0.784314
78 AZC 0.415094 0.795918
79 SN5 SN5 0.412698 0.705882
80 MBG A2G 0.412698 0.851064
81 A2G MBG 0.412698 0.851064
82 HS2 0.411765 0.8125
83 5AX 0.411765 0.866667
84 6ZC 0.409091 0.655738
85 LEC 0.409091 0.655738
86 GAL BGC NAG GAL 0.408451 0.888889
87 TCG 0.408451 0.689655
88 CTO TMX 0.408451 0.689655
89 NAG NAG NAG NAG NAG NAG NAG 0.407895 0.740741
90 BMA 0.404762 0.7
91 WOO 0.404762 0.7
92 ALL 0.404762 0.7
93 GLA 0.404762 0.7
94 MAN 0.404762 0.7
95 GAL 0.404762 0.7
96 GLC 0.404762 0.7
97 GXL 0.404762 0.7
98 GIV 0.404762 0.7
99 BGC 0.404762 0.7
100 NAG AMU 0.402778 0.8
101 NAG MUB 0.402778 0.8
102 A2G GAL FUC 0.4 0.869565
103 DR3 0.4 0.869565
104 NAG GAL FUC 0.4 0.869565
105 FUC GL0 A2G 0.4 0.869565
106 A2G GLA FUC 0.4 0.869565
107 FUC GAL A2G 0.4 0.869565
108 NGA GAL FUC 0.4 0.869565
109 FUC GLA A2G 0.4 0.869565
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4PQG; Ligand: UDP; Similar sites found: 45
This union binding pocket(no: 1) in the query (biounit: 4pqg.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1XV5 UDP 0.0001343 0.45263 1.74564
2 4GYW UDP 0.002548 0.43462 2.15264
3 5BNW 12V 0.002757 0.43435 2.15264
4 5LWV UDP 0.003009 0.42593 2.15264
5 4N3A UDP 0.004354 0.42028 2.15264
6 4N39 UDP 0.001485 0.41671 2.15264
7 1VKO NAD 0.007559 0.41349 2.15264
8 3H4T UDP 0.002835 0.41725 2.22772
9 1U1I NAD 0.01675 0.40022 2.29592
10 1RM0 D6P 0.0113 0.42104 2.34834
11 4X1T UDP 0.000155 0.45326 2.45098
12 2VCH UDP 0.0005698 0.45766 2.5
13 2IV3 UDP 0.000003706 0.53732 2.92398
14 2WTX UDP 0.00004093 0.5178 2.95359
15 2WTX VDO 0.001647 0.44308 2.95359
16 3OTI TYD 0.002638 0.41858 3.26633
17 1EM6 NBG 0.0007723 0.46983 3.5225
18 1RZU ADP 0.0002896 0.43341 3.91753
19 5TIV A3P 0.01316 0.41198 3.95257
20 4YRY NAD 0.0348 0.40072 3.98551
21 1QM5 PLP 0.00008913 0.51543 4.10959
22 3RHZ UDP 0.00288 0.41144 4.71976
23 2HQM FAD 0.02144 0.40303 4.80167
24 4RIF 3R2 0.0003282 0.4665 5.01319
25 4XSU UDP 0.000000002916 0.6843 5.6701
26 4XSU GLC 0.000000002916 0.6843 5.6701
27 3S2U UD1 0.0003186 0.45766 5.75342
28 1J39 UPG 0.0003082 0.46938 6.26781
29 2RAB FAD 0.02328 0.40304 6.47948
30 2RAB NAD 0.04287 0.40304 6.47948
31 3IAA TYD 0.001644 0.42539 7.45192
32 1RRV TYD 0.001835 0.414 7.45192
33 3RSC TYD 0.001613 0.42767 7.46988
34 3OTH CLJ 0.004125 0.43525 8.73786
35 3OTH TYD 0.003109 0.4046 8.73786
36 2IW1 U2F 0.000001718 0.56612 11.2299
37 2XA2 UPG 0.00001421 0.51511 11.7788
38 3OKP GDD 0.00000205 0.52028 11.9289
39 3CV3 UDP 0.0001841 0.45502 13.0542
40 2GEK GDP 0.00009823 0.4502 16.0099
41 3HBN UDP 0.001365 0.42156 23.7589
42 3OKA GDD 0.000006586 0.47626 23.8095
43 4X7R UDP 0.0000000001488 0.71199 30.0203
44 4X7R NTO 0.000000006998 0.68499 30.0203
45 4X7R 3YW 0.00000001694 0.6511 30.0203
Pocket No.: 2; Query (leader) PDB : 4PQG; Ligand: NAG; Similar sites found: 45
This union binding pocket(no: 2) in the query (biounit: 4pqg.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1IMB LIP 0.009202 0.41195 1.80505
2 4TXJ THM 0.02632 0.4096 2.02703
3 3NB0 G6P 0.00557 0.41516 2.15264
4 4XV1 904 0.04112 0.40165 2.39726
5 4O33 TZN 0.03263 0.41821 2.39808
6 4O33 3PG 0.03263 0.41821 2.39808
7 4EN4 ATP 0.03961 0.40755 2.5641
8 4EN4 GT0 0.03961 0.40755 2.5641
9 4EN4 GT1 0.03961 0.40755 2.5641
10 4F97 VDO 0.001771 0.46601 2.61569
11 2WTX UDP 0.000006472 0.60336 2.95359
12 2WTX VDO 0.000438 0.50474 2.95359
13 4WB7 ATP 0.00949 0.43746 2.96296
14 1DQS NAD 0.04735 0.40604 3.05344
15 1P1C SAH 0.02827 0.40011 3.13112
16 4I42 1HA 0.01825 0.41668 3.15789
17 2AE2 PTO 0.04139 0.40923 3.46154
18 2AE2 NAP 0.04139 0.40923 3.46154
19 1EM6 NBG 0.0001042 0.55059 3.5225
20 4I4Z 2NE 0.03753 0.40151 4
21 1QM5 GLC GLC GLC PO4 SGC GLC 0.00002204 0.5755 4.10959
22 1QM5 PLP 0.00004462 0.57271 4.10959
23 2RIF AMP 0.01336 0.40405 4.25532
24 1TUF AZ1 0.005499 0.43781 4.60829
25 3A6T 8OG 0.01555 0.40289 4.65116
26 2PID YSA 0.03103 0.40215 4.77528
27 1E1O LYS 0.02408 0.40652 4.96032
28 1T3Q MCN 0.0304 0.41177 5.35714
29 4XSU GLC 0.00001053 0.57767 5.6701
30 4XSU UDP 0.00002011 0.56337 5.6701
31 5LW0 AR6 0.03 0.40022 6.06061
32 1IIM TTP 0.04763 0.40322 6.50685
33 4YHQ G10 0.02387 0.41525 7.07071
34 5ODQ 9SB 0.02658 0.40292 7.14286
35 3WXB NDP 0.0306 0.40733 7.8853
36 3O26 NDP 0.03783 0.40133 8.03859
37 2IW1 U2F 0.00008678 0.53293 11.2299
38 4XB4 45D 0.01777 0.41851 11.8421
39 3A5Z KAA 0.01163 0.42273 12.0419
40 1W5F G2P 0.01957 0.41115 12.1813
41 2NXE SAM 0.01491 0.40761 18.1102
42 3HRD MCN 0.02659 0.41383 21.25
43 4X7R 3YW 0.000000002017 0.76678 30.0203
44 4X7R UDP 0.002223 0.44859 30.0203
45 4X7R NTO 0.00561 0.44828 30.0203
Pocket No.: 3; Query (leader) PDB : 4PQG; Ligand: NAG; Similar sites found: 20
This union binding pocket(no: 3) in the query (biounit: 4pqg.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2J3M ATP 0.02187 0.40035 1.36986
2 2F1K NAP 0.02363 0.40439 2.15054
3 3SSO SAH 0.0174 0.40365 2.34834
4 4CS4 ANP 0.03326 0.40793 2.55474
5 5KZD RCJ 0.005617 0.41992 3.07167
6 5UAV NDP 0.01048 0.43302 3.41615
7 5UAV TFB 0.01048 0.43302 3.41615
8 2P2V CSF 0.01409 0.41134 3.47222
9 1ZBQ NAD 0.03568 0.40125 3.66972
10 4YDD MD1 0.03663 0.42767 4.2042
11 4YDD MGD 0.03663 0.42767 4.2042
12 5G5G MCN 0.03518 0.40569 7.42358
13 4Z24 FAD 0.04798 0.40391 7.82779
14 1QO8 FAD 0.02843 0.41602 8.02348
15 4MKF AP5 0.04018 0.40545 8.29493
16 4W6Z 8ID 0.02453 0.41386 8.35735
17 1YRO GDU 0.03147 0.40822 8.94309
18 4NU0 AP5 0.03446 0.40616 10.1382
19 5X0J SEP 0.01824 0.40264 11.5702
20 5X0J AMP 0.01686 0.40264 11.5702
Pocket No.: 4; Query (leader) PDB : 4PQG; Ligand: UDP; 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: 4pqg.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4PQG; Ligand: NAG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4pqg.bio3) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4PQG; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 4pqg.bio3) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 4PQG; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 4pqg.bio3) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 4PQG; Ligand: NAG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 4pqg.bio3) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback