Receptor
PDB id Resolution Class Description Source Keywords
5M04 1.85 Å EC: 3.6.5.- STRUCTURE OF OBGE FROM ESCHERICHIA COLI ESCHERICHIA COLI DH5[ALPHA] GTPASE OBGE CGTA HYDROLASE
Ref.: STRUCTURAL AND BIOCHEMICAL ANALYSIS OF ESCHERICHIA OBGE, A CENTRAL REGULATOR OF BACTERIAL PERSISTENCE. J. BIOL. CHEM. V. 292 5871 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:401;
Valid;
none;
Kd = 0.18 uM
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:402;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5M04 1.85 Å EC: 3.6.5.- STRUCTURE OF OBGE FROM ESCHERICHIA COLI ESCHERICHIA COLI DH5[ALPHA] GTPASE OBGE CGTA HYDROLASE
Ref.: STRUCTURAL AND BIOCHEMICAL ANALYSIS OF ESCHERICHIA OBGE, A CENTRAL REGULATOR OF BACTERIAL PERSISTENCE. J. BIOL. CHEM. V. 292 5871 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5M04 Kd = 0.18 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 5M04 Kd = 0.18 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5M04 Kd = 0.18 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 161
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 9GM 0.839506 0.973684
6 GNP 0.839506 0.973684
7 G 0.828947 0.986486
8 5GP 0.828947 0.986486
9 G1R 0.82716 0.986667
10 GCP 0.82716 0.973684
11 GSP 0.817073 0.948718
12 GAV 0.797619 0.961039
13 GMV 0.792683 0.973684
14 G2P 0.77381 0.961039
15 G2R 0.770115 0.961039
16 GP2 0.756098 0.961039
17 GDC 0.747253 0.961039
18 GKE 0.747253 0.961039
19 GDD 0.747253 0.961039
20 GPG 0.741573 0.961039
21 G3D 0.732558 0.986486
22 ALF 5GP 0.729412 0.888889
23 Y9Z 0.728261 0.902439
24 G5P 0.723404 0.973684
25 GFB 0.72043 0.961039
26 GTG 0.72043 0.936709
27 GDR 0.72043 0.961039
28 G4P 0.715909 0.986486
29 G3A 0.712766 0.973684
30 6CK 0.712766 0.936709
31 GDP AF3 0.7 0.888889
32 ALF GDP 0.7 0.888889
33 GDP ALF 0.7 0.888889
34 YGP 0.698925 0.901235
35 GKD 0.697917 0.961039
36 JB2 0.697917 0.961039
37 GDX 0.690722 0.973684
38 GPD 0.690722 0.925
39 GMP 0.684211 0.88
40 0O2 0.666667 0.986486
41 JB3 0.656863 0.948718
42 NGD 0.650485 0.961039
43 DGI 0.636364 0.923077
44 GDP 7MG 0.636364 0.911392
45 U2G 0.634615 0.936709
46 GPX 0.634409 0.946667
47 G G 0.632653 0.948052
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 CG2 0.622642 0.936709
52 FEG 0.619048 0.879518
53 MGD 0.614679 0.891566
54 ZGP 0.613208 0.869048
55 GH3 0.612903 0.973333
56 3GP 0.611765 0.946667
57 MD1 0.607143 0.891566
58 PGD 0.59292 0.925
59 DGT 0.591398 0.923077
60 BGO 0.588785 0.924051
61 TPG 0.582609 0.840909
62 DBG 0.582609 0.948718
63 2GP 0.574713 0.96
64 FE9 0.570175 0.776596
65 GCP G 0.56 0.921053
66 A G 0.553571 0.935065
67 G A A A 0.553571 0.923077
68 MGP 0.553191 0.961039
69 U A G G 0.548673 0.935065
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 G1R G1R 0.542373 0.924051
73 P2G 0.527473 0.883117
74 PGD O 0.525 0.850575
75 ADP 0.522222 0.92
76 R5I 0.520833 0.946667
77 R7I 0.520833 0.946667
78 GGM 0.517544 0.901235
79 DGP 0.516484 0.910256
80 DG 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G U 0.513274 0.9
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 AKW 0.504425 0.890244
86 G C 0.504348 0.9
87 GPC 0.491525 0.879518
88 G7M 0.483871 0.948052
89 6AD 0.479592 0.841463
90 ATP 0.473684 0.92
91 HEJ 0.473684 0.92
92 G2Q 0.471154 0.961039
93 5FA 0.46875 0.92
94 AQP 0.46875 0.92
95 GTA 0.468468 0.936709
96 7DD 0.468085 0.906667
97 G G G RPC 0.466102 0.875
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 B4P 0.457447 0.894737
102 AP5 0.457447 0.894737
103 A2D 0.456522 0.894737
104 6YZ 0.455446 0.896104
105 G G G C 0.455285 0.9125
106 5GP 5GP 0.454545 0.883117
107 ANP 0.454545 0.896104
108 ACQ 0.454545 0.896104
109 AT4 0.452632 0.884615
110 A G C C 0.451613 0.911392
111 APC G U 0.45082 0.886076
112 PRT 0.449541 0.959459
113 G U34 0.449153 0.888889
114 DG DG 0.448598 0.865854
115 ITT 0.447917 0.868421
116 BA3 0.446809 0.894737
117 C2E 0.444444 0.921053
118 PCG 0.444444 0.933333
119 35G 0.444444 0.933333
120 MGO 0.441176 0.864198
121 AN2 0.4375 0.907895
122 G C C C 0.4375 0.924051
123 M33 0.43299 0.883117
124 UCG 0.429688 0.911392
125 A G U 0.42963 0.888889
126 ACP 0.428571 0.896104
127 MGQ 0.424528 0.935897
128 AR6 0.424242 0.894737
129 7DT 0.424242 0.906667
130 APR 0.424242 0.894737
131 93A 0.42268 0.833333
132 A4P 0.420168 0.869048
133 G8D 0.42 0.875
134 AD9 0.42 0.896104
135 SAP 0.42 0.873418
136 AGS 0.42 0.873418
137 CA0 0.418367 0.896104
138 ATF 0.417476 0.884615
139 AGO 0.414634 0.888889
140 A G U U 0.414286 0.888889
141 NIA 0.413043 0.82716
142 MGV 0.412844 0.890244
143 TAT 0.411765 0.884615
144 T99 0.411765 0.884615
145 ADQ 0.411215 0.871795
146 A1R 0.411215 0.839506
147 RGT 0.410714 0.909091
148 CGP 0.409836 0.86747
149 C1Z 0.409091 0.986486
150 A 0.408602 0.893333
151 AMP 0.408602 0.893333
152 UP5 0.40678 0.873418
153 AMZ 0.406593 0.918919
154 C2R 0.406593 0.906667
155 JBT 0.405882 0.778947
156 A22 0.40566 0.907895
157 25L 0.405405 0.907895
158 ADX 0.40404 0.809524
159 8OD 0.401961 0.946667
160 50T 0.4 0.883117
161 4TC 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5M04; Ligand: GDP; Similar sites found with APoc: 132
This union binding pocket(no: 1) in the query (biounit: 5m04.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 2FFQ GSP None
2 1OIV GDP 1.57068
3 5W7Q GDP 1.94444
4 1DAR GDP 2.22222
5 3VMF GTP 2.94906
6 1G7S GDP 3.05556
7 6AU6 GDP 3.05556
8 5H7J GCP 3.05556
9 5W76 GDP 3.11688
10 2C78 GNP 3.33333
11 1TQ4 GDP 3.33333
12 1Y3A GDP 3.34347
13 1TAD ALF 3.39506
14 1TAD GDP 3.39506
15 1BH2 GSP 3.49206
16 1D2E GDP 3.61111
17 3WYA GDP 3.61111
18 1SKQ GDP 3.61111
19 5W75 GDP 3.61111
20 2RCN GDP 3.63128
21 3MD0 GDP 3.66197
22 3U6B GDP 3.88889
23 5FG3 GDP 3.88889
24 4G5G GDP 3.88889
25 5YT0 GDP 3.88889
26 1D8T GDP 3.88889
27 5JBQ GDP 3.88889
28 3U6K GDP 3.88889
29 2BVN GNP 3.88889
30 5O74 GDP 4.06091
31 1G16 GDP 4.11765
32 5E95 GDP 4.16667
33 6BVJ GNP 4.19162
34 1WQ1 GDP 4.21687
35 6G14 G4P 4.42177
36 3SFV GDP 4.65116
37 5CK5 GDP 4.72222
38 6D5J GNP 4.79042
39 6BVK GNP 4.79042
40 6D5E GNP 4.79042
41 6D5H GNP 4.79042
42 6D5G GNP 4.79042
43 4B47 GDP 5
44 3T5G GDP 5.27778
45 1YVD GNP 5.32544
46 5KDO GDP 5.40541
47 3Q72 GNP 5.42169
48 1GOT GDP 5.47945
49 1F6B GDP 5.55556
50 5JCZ GDP 5.55556
51 4LC1 GDP 5.63798
52 4J0Q GDP 5.83333
53 3Q85 GNP 5.91716
54 4P3Y GDP 6.04396
55 3CNL GNP 6.38889
56 1YZG GDP 6.70391
57 1CS4 GSP 6.85279
58 1KK1 GNP 7.77778
59 1GP2 GDP 7.77778
60 1Z0F GDP 7.82123
61 3EC1 GDP 8.05556
62 5H7K GDP 8.06045
63 3T12 GDP ALF 8.08081
64 3T1O GDP 8.08081
65 6CRK GDP 8.10811
66 3M1I GTP 8.33333
67 4HDO GNP 8.38323
68 2C5L GTP 8.54701
69 1GUA GNP 8.64198
70 1Z0A GDP 9.77011
71 3DOE GTP 9.89583
72 1KSH GDP 10.2151
73 3RWO GDP 10.8108
74 1R4A GNP 10.9091
75 3N5C GDP 11.1111
76 3CPJ GDP 11.2108
77 1PUJ GNP 11.3475
78 1MKY GDP 11.6667
79 2CJW GDP 13.0208
80 5UWQ GNP 13.0802
81 5DHF GNP 13.0802
82 5UWS GNP 13.0802
83 6CIT GNP 13.0802
84 5UWP GNP 13.0802
85 5UWT GNP 13.0802
86 5UWU GNP 13.0802
87 4DKX GDP 13.4259
88 2QN6 GDP 13.9785
89 4DCT GDP 14.0351
90 3AQ4 GDP 14.1304
91 2HT6 GDP 14.3678
92 3GJ8 GDP 14.4796
93 3GJ0 GDP 14.4796
94 3GJ4 GDP 14.4796
95 4HAT GNP 14.8148
96 3CH5 GDP 14.8148
97 5BXQ GDP 14.8148
98 2EFE GNH 14.9171
99 4YLG GDP 15.0289
100 2A5J GDP 15.1832
101 3W5J GDP 15.1961
102 5EE5 GTP 15.7895
103 1S9D GDP 15.8537
104 1RE0 GDP 15.8537
105 1J2J GTP 16.2651
106 3WYG GTP 16.4835
107 1ZJ6 G3D 16.5775
108 3WYF GTP 17.2269
109 3GJ5 GDP 17.6471
110 3BC1 GNP 17.9487
111 1WA5 GTP 18.1818
112 3GJ7 GDP 18.3673
113 1YRB GDP 19.8473
114 1Z2A GDP 20.8333
115 3GJ3 GDP 21.2121
116 3TK1 GDP 23.3333
117 1VG1 GDP 28.6486
118 1VG9 GDP 28.6486
119 1S8F GDP 31.6384
120 2X77 GDP 33.3333
121 1MR3 G3D 34.8066
122 1UAD GNP 36
123 5UWH GNP 36.3636
124 3WY9 GDP 37.5
125 1U8Z GDP 37.5
126 2HCJ GDP 37.8378
127 2WJG GDP 38.8298
128 1CLU DBG 39.759
129 1FZQ GDP 41.4365
130 1SVI GDP 41.5385
131 2WJH GDP 43.9759
132 5UWO GNP 45
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