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Receptor
PDB id Resolution Class Description Source Keywords
4DEC 1.98 Å EC: 2.4.1.- CRYSTAL STRUCTURE OF GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE FR MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MN2+, URIDINE-DI( UDP) AND PHOSPHOGLYCERIC ACID (PGA) MYCOBACTERIUM TUBERCULOSIS TRANSFERASE
Ref.: MECHANISTIC INSIGHTS INTO THE RETAINING GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE FROM MYCOBACTE J.BIOL.CHEM. V. 287 24649 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PG A:403;
Valid;
none;
Kd = 4 uM
186.057 C3 H7 O7 P C([C@...
GOL A:405;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MN A:402;
Part of Protein;
none;
submit data
54.938 Mn [Mn+2...
PO4 A:404;
A:406;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
UDP A:401;
Valid;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DEC 1.98 Å EC: 2.4.1.- CRYSTAL STRUCTURE OF GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE FR MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MN2+, URIDINE-DI( UDP) AND PHOSPHOGLYCERIC ACID (PGA) MYCOBACTERIUM TUBERCULOSIS TRANSFERASE
Ref.: MECHANISTIC INSIGHTS INTO THE RETAINING GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE FROM MYCOBACTE J.BIOL.CHEM. V. 287 24649 2012
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 4DEC Kd = 4 uM 3PG C3 H7 O7 P C([C@H](C(....
2 4Y6U - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
3 4Y6N - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4DEC Kd = 4 uM 3PG C3 H7 O7 P C([C@H](C(....
2 4Y6U - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
3 4Y6N - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
4 3CKJ - CIT C6 H8 O7 C(C(=O)O)C....
5 3CKO - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 3CKV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
7 3CKN - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 4DEC Kd = 4 uM 3PG C3 H7 O7 P C([C@H](C(....
2 4Y6U - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
3 4Y6N - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
4 3CKJ - CIT C6 H8 O7 C(C(=O)O)C....
5 3CKO - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 3CKV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
7 3CKN - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3PG; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 3PG 1 1
2 DEZ 0.575758 0.941176
3 DER 0.575758 0.941176
4 SEP 0.515152 0.74359
5 4TP 0.5 0.780488
6 PA5 0.486486 0.941176
7 R10 0.486486 0.941176
8 DG2 0.485714 0.909091
9 LG6 0.461538 0.941176
10 6PG 0.461538 0.941176
11 HG3 0.451613 0.9375
12 1GP 0.4375 0.852941
13 G3P 0.4375 0.852941
14 PGA 0.433333 0.90625
15 DXP 0.432432 0.911765
16 GOS 0.424242 0.857143
17 M2P 0.424242 0.857143
18 G3H 0.411765 0.9375
19 5SP 0.410256 0.837838
20 D5X 0.410256 0.941176
21 HMS 0.410256 0.837838
22 5RP 0.410256 0.837838
23 0V5 0.40625 0.727273
24 PEQ 0.40625 0.727273
25 RUB 0.4 0.885714
26 XBP 0.4 0.885714
27 RES 0.4 0.659574
Ligand no: 2; Ligand: UDP; Similar ligands found: 117
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 U 0.78125 0.984615
6 UPU 0.72973 0.940298
7 2KH 0.722222 0.970149
8 44P 0.720588 0.955882
9 UFM 0.717949 0.941176
10 GDU 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GUD 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UPP 0.705128 0.941176
17 UDH 0.705128 0.864865
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UPF 0.691358 0.888889
21 UAD 0.670732 0.941176
22 UDX 0.670732 0.941176
23 3UC 0.658824 0.888889
24 USQ 0.654762 0.820513
25 UGB 0.654762 0.955224
26 UGA 0.654762 0.955224
27 G3N 0.647059 0.914286
28 UDM 0.636364 0.914286
29 URI 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 Y6W 0.607143 0.888889
33 CDP 0.605263 0.942029
34 HP7 0.591398 0.941176
35 UD7 0.591398 0.927536
36 MJZ 0.585106 0.914286
37 IUG 0.583333 0.810127
38 F5G 0.578947 0.927536
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 F5P 0.578947 0.914286
42 UD4 0.578947 0.914286
43 CJB 0.573529 0.820895
44 UDZ 0.571429 0.853333
45 DUD 0.571429 0.913043
46 UP5 0.571429 0.853333
47 U U 0.563218 0.955224
48 EPZ 0.56 0.914286
49 5GW 0.559524 0.942029
50 EPU 0.554455 0.901408
51 EEB 0.554455 0.901408
52 U3P 0.547945 0.939394
53 UA3 0.547945 0.939394
54 4TC 0.544554 0.831169
55 HF4 0.54321 0.942029
56 CTP 0.54321 0.942029
57 CSQ 0.531915 0.851351
58 CSV 0.531915 0.851351
59 DUT 0.52439 0.913043
60 4GW 0.516484 0.915493
61 UMA 0.513761 0.914286
62 U4S 0.513158 0.753425
63 U2P 0.506667 0.954545
64 U2S 0.5 0.767123
65 U3S 0.5 0.753425
66 PUP 0.48913 0.913043
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 U22 0.486957 0.790123
70 DKX 0.486486 0.746479
71 U1S 0.482759 0.75
72 A U 0.481132 0.805195
73 2QR 0.478632 0.822785
74 5FU 0.474359 0.914286
75 G U 0.472222 0.7875
76 8OD 0.47191 0.851351
77 C5G 0.468085 0.888889
78 7XL 0.465909 0.888889
79 U U U U 0.461538 0.940298
80 UMF 0.461538 0.857143
81 G8D 0.460674 0.855263
82 UTP U U U 0.456522 0.895522
83 2TU 0.452055 0.774648
84 4RA 0.451613 0.855263
85 C2G 0.450549 0.901408
86 DU 0.45 0.898551
87 UMP 0.45 0.898551
88 C 0.45 0.927536
89 CAR 0.45 0.927536
90 C5P 0.45 0.927536
91 UAG 0.448 0.864865
92 CDC 0.446809 0.777778
93 5BU 0.444444 0.914286
94 UD0 0.444444 0.844156
95 N3E 0.440476 0.733333
96 UC5 0.440476 0.9
97 UUA 0.438356 0.772727
98 DUP 0.431818 0.887324
99 2GW 0.431373 0.901408
100 M7G 0.430108 0.780488
101 CNU 0.428571 0.927536
102 CDM 0.427083 0.842105
103 H6Y 0.425532 0.851351
104 16B 0.421687 0.888889
105 S5P 0.419753 0.915493
106 8GT 0.419355 0.855263
107 CXY 0.418367 0.888889
108 UPA 0.418182 0.842105
109 U2G 0.410714 0.822785
110 U A A U 0.409836 0.842105
111 UML 0.408759 0.810127
112 UP6 0.407407 0.871429
113 M7M 0.40625 0.771084
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
117 PMP UD1 0.401575 0.7875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DEC; Ligand: UDP; Similar sites found with APoc: 113
This union binding pocket(no: 1) in the query (biounit: 4dec.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 4TQK NAG 1.45349
2 1RJW ETF 1.47493
3 5VCM UDP 1.74419
4 1YQT ADP 1.74419
5 1PDZ PGA 1.74419
6 1FWY UD1 1.81269
7 2JK0 ASP 1.84615
8 4L80 OXL 2.03488
9 2YQS UD1 2.32558
10 5V7I 8Z1 2.32558
11 4IRP UDP 2.39044
12 4WZ6 ATP 2.41379
13 3DX5 DHB 2.44755
14 2PEL LBT 2.54237
15 2ATJ BHO 2.5974
16 1KJ8 GAR 2.61628
17 2PZE ATP 2.62009
18 5NM7 GLY 2.63158
19 1LVW TYD 2.71186
20 1VRP IOM 2.88714
21 3KAL HGS 2.90698
22 2AWN ADP 2.90698
23 3ZF8 GDP 2.95082
24 1JE1 GMP 2.9661
25 4DDY DN6 3.04183
26 6ACS CIT 3.10078
27 4PPF FLC 3.19767
28 4ARU TLA 3.19767
29 2P6W FLC 3.28639
30 1H5R THM 3.41297
31 1H5S TMP 3.41297
32 1HV9 UD1 3.48837
33 5JVB 2PO 3.57143
34 1C9K 5GP 3.77907
35 5TKL G3H 3.77907
36 2CBZ ATP 3.79747
37 2WQ4 SFU 3.84615
38 5LV1 78T 3.92857
39 5O2J 2PO 4.0293
40 1U6R IOM 4.06977
41 1ZDQ MSM 4.06977
42 1O5O U5P 4.0724
43 3MA0 XYP 4.15335
44 2Y6P CTP 4.2735
45 2J0B UDP 4.28571
46 3QTP 2PG 4.36047
47 4U00 ADP 4.65116
48 1TL2 NDG 4.66102
49 3SUC ATP 4.66321
50 1V84 UDP 4.74308
51 4YJK URA 4.7619
52 4G86 BNT 4.92958
53 3QH2 3NM 4.97738
54 1JJ7 ADP 5
55 1QVJ RP5 5.13699
56 1L7N AF3 5.21327
57 1L7N ALF 5.21327
58 2FFU UDP 5.52326
59 1ODJ GMP 5.53191
60 3W6G FLC 5.55556
61 5CDH TLA 5.65476
62 3FSY SCA 5.72289
63 1JV1 UD1 5.81395
64 3N2O AG2 5.81395
65 2APC UDM 5.84795
66 5YV5 ADP 6.10465
67 2FKA BEF 6.20155
68 3OID TCL 6.20155
69 3ITJ CIT 6.21302
70 1G6H ADP 6.22568
71 5WKR NAR 6.27803
72 2OG2 MLI 6.39535
73 2J5V PCA 6.39535
74 5HS2 CTP 6.46552
75 1I52 CTP 6.77966
76 3K8D CTP 6.81818
77 3E4O SIN 6.88525
78 3B9Q MLI 7.28477
79 3CU0 UDP 7.82918
80 2YIP YIO 7.97101
81 1H7F C5P 8.16327
82 3KIH GDL 8.24742
83 5AJP UDP 8.43023
84 5NDF UDP 8.43023
85 5NDF LU2 8.43023
86 1OJJ GLC GAL 8.72093
87 1OJK GLC BGC 8.72093
88 3OH3 UAD 8.72093
89 2BES RES 8.72093
90 2X9L BOG 8.79121
91 4YEE 4CQ 8.88889
92 2D2F ADP 9.2
93 5WUU 7UU 9.35252
94 1YP4 ADP 9.88372
95 3RV5 DXC 10.1124
96 3SHR CMP 10.7023
97 2XWL CTP 10.7623
98 5F7J ADE 12.2093
99 3W9F I3P 12.3077
100 1W55 C 12.5
101 4IF4 BEF 12.5
102 3HY2 ATP 12.7273
103 6H21 UD1 12.7907
104 2D7I UDP 13.3721
105 4RW3 IPD 13.5762
106 2QGI UDP 14.9194
107 2PA4 UPG 15.1703
108 3AJM 4IP 16.4319
109 2BO4 FLC 18.314
110 4K7O EKZ 19.0476
111 1QGQ UDP 25.4902
112 5MM0 GDD 27.6163
113 6H0B UDP 31.25
Pocket No.: 2; Query (leader) PDB : 4DEC; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4dec.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4DEC; Ligand: 3PG; Similar sites found with APoc: 113
This union binding pocket(no: 3) in the query (biounit: 4dec.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 4TQK NAG 1.45349
2 1RJW ETF 1.47493
3 5VCM UDP 1.74419
4 1YQT ADP 1.74419
5 1PDZ PGA 1.74419
6 1FWY UD1 1.81269
7 2JK0 ASP 1.84615
8 4L80 OXL 2.03488
9 2YQS UD1 2.32558
10 5V7I 8Z1 2.32558
11 4IRP UDP 2.39044
12 4WZ6 ATP 2.41379
13 3DX5 DHB 2.44755
14 2PEL LBT 2.54237
15 2ATJ BHO 2.5974
16 1KJ8 GAR 2.61628
17 2PZE ATP 2.62009
18 5NM7 GLY 2.63158
19 1LVW TYD 2.71186
20 1VRP IOM 2.88714
21 3KAL HGS 2.90698
22 2AWN ADP 2.90698
23 3ZF8 GDP 2.95082
24 1JE1 GMP 2.9661
25 4DDY DN6 3.04183
26 6ACS CIT 3.10078
27 4PPF FLC 3.19767
28 4ARU TLA 3.19767
29 2P6W FLC 3.28639
30 1H5R THM 3.41297
31 1H5S TMP 3.41297
32 1HV9 UD1 3.48837
33 5JVB 2PO 3.57143
34 1C9K 5GP 3.77907
35 5TKL G3H 3.77907
36 2CBZ ATP 3.79747
37 2WQ4 SFU 3.84615
38 5LV1 78T 3.92857
39 5O2J 2PO 4.0293
40 1U6R IOM 4.06977
41 1ZDQ MSM 4.06977
42 1O5O U5P 4.0724
43 3MA0 XYP 4.15335
44 2Y6P CTP 4.2735
45 2J0B UDP 4.28571
46 3QTP 2PG 4.36047
47 4U00 ADP 4.65116
48 1TL2 NDG 4.66102
49 3SUC ATP 4.66321
50 1V84 UDP 4.74308
51 4YJK URA 4.7619
52 4G86 BNT 4.92958
53 3QH2 3NM 4.97738
54 1JJ7 ADP 5
55 1QVJ RP5 5.13699
56 1L7N AF3 5.21327
57 1L7N ALF 5.21327
58 2FFU UDP 5.52326
59 1ODJ GMP 5.53191
60 3W6G FLC 5.55556
61 5CDH TLA 5.65476
62 3FSY SCA 5.72289
63 1JV1 UD1 5.81395
64 3N2O AG2 5.81395
65 2APC UDM 5.84795
66 5YV5 ADP 6.10465
67 2FKA BEF 6.20155
68 3OID TCL 6.20155
69 3ITJ CIT 6.21302
70 1G6H ADP 6.22568
71 5WKR NAR 6.27803
72 2OG2 MLI 6.39535
73 2J5V PCA 6.39535
74 5HS2 CTP 6.46552
75 1I52 CTP 6.77966
76 3K8D CTP 6.81818
77 3E4O SIN 6.88525
78 3B9Q MLI 7.28477
79 3CU0 UDP 7.82918
80 2YIP YIO 7.97101
81 1H7F C5P 8.16327
82 3KIH GDL 8.24742
83 5AJP UDP 8.43023
84 5NDF UDP 8.43023
85 5NDF LU2 8.43023
86 1OJJ GLC GAL 8.72093
87 1OJK GLC BGC 8.72093
88 3OH3 UAD 8.72093
89 2BES RES 8.72093
90 2X9L BOG 8.79121
91 4YEE 4CQ 8.88889
92 2D2F ADP 9.2
93 5WUU 7UU 9.35252
94 1YP4 ADP 9.88372
95 3RV5 DXC 10.1124
96 3SHR CMP 10.7023
97 2XWL CTP 10.7623
98 5F7J ADE 12.2093
99 3W9F I3P 12.3077
100 1W55 C 12.5
101 4IF4 BEF 12.5
102 3HY2 ATP 12.7273
103 6H21 UD1 12.7907
104 2D7I UDP 13.3721
105 4RW3 IPD 13.5762
106 2QGI UDP 14.9194
107 2PA4 UPG 15.1703
108 3AJM 4IP 16.4319
109 2BO4 FLC 18.314
110 4K7O EKZ 19.0476
111 1QGQ UDP 25.4902
112 5MM0 GDD 27.6163
113 6H0B UDP 31.25
Pocket No.: 4; Query (leader) PDB : 4DEC; Ligand: 3PG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4dec.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
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