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Receptor
PDB id Resolution Class Description Source Keywords
1S89 2.22 Å EC: 4.2.3.3 H98N MUTANT OF METHYLGLYOXAL SYNTHASE FROM E. COLI COMPLEXED WITH PHOSPHOGLYCOLIC ACID ESCHERICHIA COLI GLYCOLYTIC BYPASS METHYLGLYOXAL LYASE
Ref.: MUTAGENIC STUDIES ON HISTIDINE 98 OF METHYLGLYOXAL SYNTHASE: EFFECTS ON MECHANISM AND CONFORMATIONAL CHANGE. BIOCHEMISTRY V. 43 3802 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PGA A:201;
B:202;
C:203;
D:204;
E:205;
F:206;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Ki = 5.8 uM
156.031 C2 H5 O6 P C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1IK4 2 Å EC: 4.2.3.3 X-RAY STRUCTURE OF METHYLGLYOXAL SYNTHASE FROM E. COLI COMPLEXED WITH PHOSPHOGLYCOLOHYDROXAMIC ACID ESCHERICHIA COLI GLYCOLYTIC BYPASS METHYLGLYOXAL LYASE
Ref.: MECHANISTIC IMPLICATIONS OF METHYLGLYOXAL SYNTHASE COMPLEXED WITH PHOSPHOGLYCOLOHYDROXAMIC ACID AS OBSERVED BY X-RAY CRYSTALLOGRAPHY AND NMR SPECTROSCOPY. BIOCHEMISTRY V. 40 6805 2001
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1S89 Ki = 5.8 uM PGA C2 H5 O6 P C(C(=O)O)O....
2 1EGH Ki = 2 uM PGA C2 H5 O6 P C(C(=O)O)O....
3 1S8A Ki ~ 74 uM PGA C2 H5 O6 P C(C(=O)O)O....
4 1IK4 Ki = 39 nM PGH C2 H6 N O6 P C(C(=O)NO)....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1S89 Ki = 5.8 uM PGA C2 H5 O6 P C(C(=O)O)O....
2 1EGH Ki = 2 uM PGA C2 H5 O6 P C(C(=O)O)O....
3 1S8A Ki ~ 74 uM PGA C2 H5 O6 P C(C(=O)O)O....
4 1IK4 Ki = 39 nM PGH C2 H6 N O6 P C(C(=O)NO)....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1S89 Ki = 5.8 uM PGA C2 H5 O6 P C(C(=O)O)O....
2 1EGH Ki = 2 uM PGA C2 H5 O6 P C(C(=O)O)O....
3 1S8A Ki ~ 74 uM PGA C2 H5 O6 P C(C(=O)O)O....
4 1IK4 Ki = 39 nM PGH C2 H6 N O6 P C(C(=O)NO)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PGA; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 PGA 1 1
2 HPV 0.555556 0.903226
3 13P 0.5 0.818182
4 PGH 0.482759 0.651163
5 3PG 0.433333 0.90625
6 3PP 0.423077 0.866667
7 PAE 0.416667 0.806452
8 EFS 0.416667 0.741935
9 SEP 0.40625 0.710526
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1IK4; Ligand: PGH; Similar sites found with APoc: 156
This union binding pocket(no: 1) in the query (biounit: 1ik4.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3LN9 FLC None
2 1MJH ATP None
3 3OCP CMP None
4 2CB3 MLD 1.31579
5 4PXL NAD 1.97368
6 3RHJ NAP 2.63158
7 3QF7 ANP 2.63158
8 1G8S MET 2.63158
9 5KF6 NAD 3.28947
10 1O9J NAD 3.28947
11 6B5G NAD 3.28947
12 6B5G CQY 3.28947
13 2CBZ ATP 3.28947
14 3HAZ NAD 3.28947
15 4P83 U5P 3.28947
16 5LV1 78T 3.28947
17 4ZUL UN1 3.28947
18 4K7O EKZ 3.28947
19 5XK9 DMA 3.28947
20 2ZWS PLM 3.28947
21 2GJN NIS 3.28947
22 3JZ4 NAP 3.28947
23 4NTD FAD 3.28947
24 4U00 ADP 3.28947
25 4I8P NAD 3.94737
26 4GKY MAN 3.94737
27 6MVU K4V 3.94737
28 1KY8 NAP 3.94737
29 4I9B NAD 3.94737
30 3IWJ NAD 3.94737
31 4A0M NAD 3.94737
32 5G3U FDA 3.94737
33 4URN NOV 3.94737
34 5ZBC FAD 3.94737
35 2C42 TPP 3.94737
36 2C42 PYR 3.94737
37 5G3U ITW 3.94737
38 2IMP NAI 3.94737
39 4MO2 FDA 3.94737
40 4PZ2 NAD 4.60526
41 5IUW NAD 4.60526
42 5IUW IAC 4.60526
43 5AO7 NAG 4.60526
44 5N5S NAP 4.60526
45 2Z48 A2G 4.60526
46 4JCA CIT 4.60526
47 1BH2 GSP 4.60526
48 4CQM NAP 4.60526
49 1FFU CDP 5.26316
50 5GVR LMR 5.26316
51 2ZXI FAD 5.26316
52 4YAG NAI 5.26316
53 3NYQ MCA 5.26316
54 3NYQ AMP 5.26316
55 3QDK QDK 5.26316
56 5WS9 AMP 5.26316
57 4C2C ALA ALA ALA 5.26316
58 4A1O JLN 5.26316
59 1G6H ADP 5.26316
60 2V2G BEZ 5.26316
61 2AWN ADP 5.26316
62 3QDT A2G GAL 5.59441
63 3QDY A2G GAL 5.59441
64 3QDX A2G GAL 5.59441
65 3QDW A2G 5.59441
66 3KIF GDL 5.66038
67 1EXF GLY 5.92105
68 5F7V GLC GLC GLC GLC 5.92105
69 4R74 F6P 5.92105
70 5F7R GLC GLC 5.92105
71 4JGT PYR 5.92105
72 3T12 GDP ALF 5.92105
73 4NU0 AP5 5.92105
74 2R4J FAD 6.57895
75 2R4J 13P 6.57895
76 1YQT ADP 6.57895
77 4U8P FDA 6.57895
78 1O5Q PYR 6.57895
79 2GCG NDP 6.57895
80 4U8P UDP 6.57895
81 2F5Z FAD 6.57895
82 5EZ7 FAD 6.57895
83 1I8T FAD 6.57895
84 1P4A PCP 6.57895
85 4YJI TYL 6.57895
86 3HGM ATP 6.80272
87 5YV5 ADP 7.23684
88 1DNP FAD 7.23684
89 3QKT ANP 7.23684
90 2OGA PGU 7.23684
91 1XX6 ADP 7.23684
92 6FK3 PPI 7.23684
93 4I3V NAD 7.23684
94 1F2U ATP 7.43243
95 1T36 U 7.89474
96 1WD4 AHR 7.89474
97 5UY8 AMZ 7.89474
98 1RRC ADP 7.89474
99 6C0B MLI 7.89474
100 1BKJ FMN 7.89474
101 5XWC 8GL 7.89474
102 5XWC 2IT 7.89474
103 5XWC NAP 7.89474
104 3QOX SAH 7.89474
105 2PZE ATP 7.89474
106 4BAS GNP 7.89474
107 4UP4 GAL NAG 7.89474
108 4PPF FLC 8.55263
109 5L13 6ZE 8.55263
110 1IY8 NAD 8.55263
111 1Z0K GTP 8.69565
112 2BJK NAD 9.21053
113 3WYF GTP 9.86842
114 4HAT GNP 9.86842
115 5UWW GNP 9.86842
116 6CIT GNP 9.86842
117 5DI9 GNP 9.86842
118 5DIF GNP 9.86842
119 3M1I GTP 9.86842
120 5UWU GNP 9.86842
121 5UWJ GNP 9.86842
122 5DHF GNP 9.86842
123 5UWO GNP 9.86842
124 5UWI GNP 9.86842
125 5UWT GNP 9.86842
126 5UWR GNP 9.86842
127 5UWQ GNP 9.86842
128 5UWS GNP 9.86842
129 1IGW PYR 9.86842
130 5UWH GNP 9.86842
131 3ICR FAD 9.86842
132 4ZOH MCN 10.5263
133 1RM6 FAD 10.5263
134 2A2C ADP 10.5263
135 2A2C NG1 10.5263
136 4WZ6 ATP 10.5263
137 5VLQ ANP 10.5263
138 2E7Z MGD 11.1842
139 1T90 NAD 11.1842
140 5EXE 5SR 11.1842
141 4YRY FAD 11.1842
142 5WKC AUJ 11.8421
143 5BSH PRO 11.8421
144 1VPE ANP 11.8421
145 3IAE D7K 11.8421
146 2WOX NDP 12.5
147 2WME NAP 12.5
148 1M1B SPV 12.5
149 1WA5 GTP 13.1579
150 1QNF HDF 14.4737
151 1QNF FAD 14.4737
152 3QVP FAD 15.1316
153 1GPE FAD 16.4474
154 3RUV ANP 18.4211
155 3WYG GTP 19.7368
156 3GJX GTP 32.2368
Pocket No.: 2; Query (leader) PDB : 1IK4; Ligand: PGH; Similar sites found with APoc: 25
This union binding pocket(no: 2) in the query (biounit: 1ik4.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2ZFZ ARG None
2 2APH AMU ALA GMA LYS DAL DAL NH2 1.31579
3 6AMI TRP 2.63158
4 5XK9 GST 3.28947
5 4MO2 FAD 3.94737
6 3HDY GDU 3.94737
7 3HDY FAD 3.94737
8 1FL2 FAD 3.94737
9 3LZW NAP 4.60526
10 1RJW ETF 4.60526
11 1JJ7 ADP 4.60526
12 1GPJ CIT 5.92105
13 1PHP ADP 5.92105
14 3ITJ CIT 6.57895
15 5N5U AMP 6.57895
16 1U3D FAD 6.57895
17 2I3G NAP 7.23684
18 5H68 AGS 7.23684
19 1GTE FAD 10.5263
20 1MDZ DCS 11.1842
21 1ZUW DGL 11.8421
22 2JK0 ASP 11.8421
23 1ZGS XMM 13.1579
24 5B48 TDN 15.1316
25 1T3D CYS 20.3947
Pocket No.: 3; Query (leader) PDB : 1IK4; Ligand: PGH; Similar sites found with APoc: 20
This union binding pocket(no: 3) in the query (biounit: 1ik4.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3FPZ AHZ 2.63158
2 3CTY FAD 3.28947
3 2J07 HDF 4.60526
4 2J07 FAD 4.60526
5 2D2F ADP 4.60526
6 2UUU FAD 5.26316
7 4TQK NAG 5.92105
8 3ITJ FAD 6.57895
9 3I7S PYR 6.57895
10 2BNE U5P 6.57895
11 5EHS 2JJ 6.57895
12 5EHS 5OY 6.57895
13 3SM2 478 9.09091
14 4D5G TPP 9.21053
15 4D5G FAD 9.21053
16 3ICS FAD 9.86842
17 2NUO BGC 13.1148
18 5K8S CMP 14.8649
19 6F9Q NAD 15.7895
20 3P13 RIP 16.6667
Pocket No.: 4; Query (leader) PDB : 1IK4; Ligand: PGH; Similar sites found with APoc: 8
This union binding pocket(no: 4) in the query (biounit: 1ik4.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2FKA BEF None
2 2BME GNP None
3 5X40 ACP 1.97368
4 5L2M 6ZY 3.28947
5 3RNM FAD 5.26316
6 5HDJ FMN 6.57895
7 4OVZ P85 7.23684
8 1NAA ABL 9.86842
Pocket No.: 5; Query (leader) PDB : 1IK4; Ligand: PGH; Similar sites found with APoc: 4
This union binding pocket(no: 5) in the query (biounit: 1ik4.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4YSX FAD 5.92105
2 5JCA FAD 7.23684
3 6BII NAP 10.5263
4 2GUD MAN 13.1148
Pocket No.: 6; Query (leader) PDB : 1IK4; Ligand: PGH; Similar sites found with APoc: 9
This union binding pocket(no: 6) in the query (biounit: 1ik4.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4HZ0 1AV None
2 5JCM FAD 2.63158
3 5J60 FAD 3.94737
4 1V8K ANP 4.60526
5 4WCX MET 7.89474
6 4UP3 FAD 9.21053
7 4YRY NAD 11.1842
8 6EJI UD2 15.7895
9 5UWP GNP 36.8421
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