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Receptor
PDB id Resolution Class Description Source Keywords
4XJ6 2.31 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ESCHERICHIA COLI DNCV 3'-DEOXY GTP BOUN ESCHERICHIA COLI CYCLIC GMP-AMP SYNTHASE BACTERIAL VIRULENCE NUCLEOTIDYLTRA
Ref.: STRUCTURAL BASIS FOR THE CATALYTIC MECHANISM OF DNC BACTERIAL HOMOLOG OF CYCLIC GMP-AMP SYNTHASE STRUCTURE V. 23 843 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:501;
A:502;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
GH3 A:503;
A:504;
Valid;
Valid;
none;
Atoms found LESS than expected: % Diff = 0;
submit data
507.181 C10 H16 N5 O13 P3 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4XJ6 2.31 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ESCHERICHIA COLI DNCV 3'-DEOXY GTP BOUN ESCHERICHIA COLI CYCLIC GMP-AMP SYNTHASE BACTERIAL VIRULENCE NUCLEOTIDYLTRA
Ref.: STRUCTURAL BASIS FOR THE CATALYTIC MECHANISM OF DNC BACTERIAL HOMOLOG OF CYCLIC GMP-AMP SYNTHASE STRUCTURE V. 23 843 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4XJ6 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4XJ6 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
2 4XJ3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4TY0 - 38V MG n/a n/a
4 4U0M - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
5 4U0N - TLL C25 H32 N8 O9 CN1[C@H](C....
6 4U03 ic50 = 1.69 uM TLL C25 H32 N8 O9 CN1[C@H](C....
7 4XJ4 - 3AT C10 H16 N5 O12 P3 c1nc(c2c(n....
8 4XJ5 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 4XJ6 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
2 4XJ3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4TY0 - 38V MG n/a n/a
4 4U0M - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
5 4U0N - TLL C25 H32 N8 O9 CN1[C@H](C....
6 4U03 ic50 = 1.69 uM TLL C25 H32 N8 O9 CN1[C@H](C....
7 4XJ4 - 3AT C10 H16 N5 O12 P3 c1nc(c2c(n....
8 4XJ5 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GH3; Similar ligands found: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 GH3 1 1
2 GTP 0.681319 0.973333
3 DGT 0.673913 0.948052
4 0O2 0.642857 0.986486
5 GP3 0.619565 0.948052
6 GDP 0.612903 0.973333
7 DGI 0.595745 0.948052
8 GSP 0.581633 0.924051
9 GAV 0.57 0.935897
10 G4P 0.57 0.986486
11 G3D 0.565657 0.986486
12 3AT 0.5625 0.92
13 GNH 0.556701 0.960526
14 G1R 0.555556 0.960526
15 G2R 0.553398 0.961039
16 GNP 0.55 0.948052
17 9GM 0.55 0.948052
18 5GP 0.542553 0.96
19 G 0.542553 0.96
20 GCP 0.54 0.973684
21 GPX 0.533981 0.946667
22 GPD 0.531532 0.925
23 G5P 0.527273 0.948052
24 GTG 0.522936 0.9125
25 G2P 0.519608 0.961039
26 G3A 0.518182 0.948052
27 6CK 0.518182 0.9125
28 DG 0.515789 0.935065
29 DGP 0.515789 0.935065
30 GP2 0.515152 0.961039
31 GMV 0.514852 0.948052
32 GDD 0.513761 0.935897
33 GKE 0.513761 0.935897
34 GDC 0.513761 0.935897
35 2GP 0.505263 0.96
36 3GP 0.505263 0.946667
37 Y9Z 0.5 0.902439
38 GFB 0.495495 0.935897
39 GDR 0.495495 0.935897
40 GPG 0.490741 0.935897
41 GMP 0.488889 0.855263
42 JB2 0.482456 0.935897
43 GKD 0.482456 0.935897
44 P2G 0.479592 0.883117
45 NGD 0.478992 0.935897
46 GDX 0.478261 0.948052
47 ALF 5GP 0.471154 0.865854
48 P1G 0.47 0.896104
49 BGO 0.466667 0.924051
50 YGP 0.464286 0.878049
51 GDP AF3 0.458716 0.865854
52 GDP ALF 0.458716 0.865854
53 ALF GDP 0.458716 0.865854
54 JB3 0.458333 0.924051
55 TPG 0.457364 0.820225
56 CAG 0.456 0.858824
57 G1G 0.448819 0.901235
58 GCP G 0.446429 0.921053
59 2MD 0.443548 0.869048
60 PGD 0.44186 0.901235
61 DG DG 0.4375 0.888889
62 MGP 0.433962 0.935897
63 MGD 0.433071 0.869048
64 GGM 0.432 0.901235
65 U2G 0.430894 0.9125
66 MD1 0.430769 0.891566
67 6G0 0.429907 0.935897
68 CG2 0.424 0.9125
69 GDP 7MG 0.423729 0.8875
70 SGP 0.421569 0.82716
71 FEG 0.419355 0.879518
72 G G 0.418803 0.923077
73 ZGP 0.416 0.869048
74 01G 0.413793 0.879518
75 DBG 0.413534 0.924051
76 CGP 0.412698 0.890244
77 C1Z 0.412281 0.986486
78 GPC 0.410853 0.857143
79 DTP 0.401869 0.858974
80 5GP 5GP 0.401869 0.883117
81 DDS 0.401869 0.810127
82 FE9 0.401515 0.757895
83 3ZE 0.4 0.884615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4XJ6; Ligand: GH3; Similar sites found with APoc: 16
This union binding pocket(no: 1) in the query (biounit: 4xj6.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2Q0D ATP 1.41643
2 5U8U FAD 1.7199
3 3JYY PPV 2.43902
4 1UDY CS8 2.77778
5 1UDY FAD 2.77778
6 3HJ1 UTP 2.84238
7 3HIY UTP 2.86458
8 4NKT 2KH 2.93255
9 2B56 UTP 3.1941
10 2B56 U5P 3.1941
11 1R89 CTP 3.4398
12 3JZ0 APC 4.1769
13 3ER9 3AT 4.1769
14 5I49 2KH 4.6683
15 5W0N 2KH 5.21092
16 1KNY APC 6.32411
Pocket No.: 2; Query (leader) PDB : 4XJ6; Ligand: GH3; Similar sites found with APoc: 126
This union binding pocket(no: 2) in the query (biounit: 4xj6.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 2YFO GAL 1.2285
2 2YFO GLA 1.2285
3 2JLD AG1 1.4742
4 3AMN CBK 1.50943
5 3AMN CBI 1.50943
6 3SXS PP2 1.7199
7 4WNK 453 1.7199
8 1XC6 GAL 1.7199
9 4YZC STU 1.7284
10 4D52 GIV 1.90476
11 3RWP ABQ 1.92926
12 8CGT TM6 1.9656
13 1YKJ FAD 2.03046
14 1QIN GIP 2.18579
15 4L9I 8PR 2.2113
16 5EW9 5VC 2.21402
17 3FW3 ETS 2.25564
18 2PI8 NAG NAG NAG NAG NAG NAG 2.31884
19 5A6N U7E 2.4735
20 5N87 N66 2.55591
21 5JKG 6LF 2.57235
22 4KU7 PCG 2.61438
23 2Q8Z NUP 2.63158
24 2V1O COA 2.64901
25 5AE9 OKO 2.7027
26 4HWS 1B3 2.7027
27 2H6T IVA VAL VAL STA ALA STA 2.7027
28 6EZ6 C5Z 2.7027
29 5EH0 5NW 2.71318
30 4PVV HO4 2.77778
31 5UFS 1TA 2.82258
32 5DX9 T6P 2.8481
33 1RE8 BD2 2.85714
34 5X8I SQZ 2.89017
35 4QTB 38Z 2.89474
36 4ZL4 4PK 2.9484
37 2XN2 GLA 2.9484
38 2HZY DHJ 2.9484
39 5JAX 6J7 2.96296
40 5BVE 4VG 3.04709
41 2B9H ADP 3.11615
42 2B9F ADP 3.11615
43 3HAZ FAD 3.1941
44 1UPA TPP 3.1941
45 2FB3 GTP 3.23529
46 4XDA ADP 3.23625
47 4XDA RIB 3.23625
48 1UAS GLA 3.31492
49 5W4W 9WG 3.32326
50 5EYG NAP 3.39623
51 3UDZ ADP 3.4398
52 2TPS TPS 3.4398
53 1TFZ 869 3.4398
54 1N5S ADL 3.57143
55 4Y85 499 3.61446
56 4RD0 GDP 3.6855
57 5XVG 8FX 3.75427
58 4O67 1SY 3.85675
59 5Y72 DST 3.8806
60 2WA4 069 3.9312
61 1ZHX HC3 3.9312
62 1UZH CAP 3.9312
63 2RHQ GAX 4.08163
64 6A1G 9OL 4.16667
65 2JG1 TA6 4.1769
66 4IJP 1EH 4.18994
67 2GJ5 VD3 4.32099
68 1WUB OTP 4.49438
69 4FFG LBS 4.6683
70 1VA6 ADP 4.6683
71 1VA6 P2S 4.6683
72 3HMO STU 4.67836
73 1KGI T4A 4.72441
74 3JRS A8S 4.80769
75 1ZAP A70 4.914
76 5DEP UD1 4.914
77 5EOB 5QQ 5.01567
78 5W0N UPU 5.21092
79 2I6A 5I5 5.21739
80 4RW3 IPD 5.40541
81 4OFG PCG 5.55556
82 2YKL NLD 5.55556
83 6C1S EFV 5.65111
84 2XIQ MLC 5.65111
85 1GQ2 NAP 5.65111
86 5C8W PCG 6.29371
87 4EN4 ATP 6.41026
88 4EN4 GT0 6.41026
89 4EN4 GT1 6.41026
90 1KJ1 MAN 6.42202
91 2A4W BLM 6.52174
92 4LNP VAL PRO PRO PRO ARG PRO PRO PRO PRO GLU 6.55738
93 5VC5 96M 6.57439
94 3VHE 42Q 6.63391
95 4OAV ACP 6.63391
96 2Y5S 78H 6.80272
97 6C0T EE4 6.91643
98 4PSB GA3 7.09677
99 5JIL 6KL 7.2165
100 5TKJ ALA VAL GLY ILE GLY ALA VAL PHE 7.30594
101 3SHR CMP 7.35786
102 4AG8 AXI 7.59494
103 5TA6 79D 7.61671
104 3FC2 IBI 7.61671
105 2V68 CAP 7.85714
106 1IR2 CAP 7.85714
107 5UWA 8ND 7.88177
108 1SDW IYT 7.96178
109 5ODY 9SK 7.97101
110 4I4B 1CV 8.59951
111 1LO8 4CA 9.21986
112 5ISY NAD 9.26641
113 4O9S 2RY 9.30233
114 1JIF CU BLM 9.83607
115 2PVN P63 9.94318
116 1UZD CAP 10.4478
117 3BJK CIT 11.3022
118 1RBO CAP 13.0081
119 1IR1 CAP 13.0081
120 3EYA FAD 13.2678
121 2XMY CDK 13.4228
122 3BZ3 YAM 15.2174
123 1LSS NAD 15.7143
124 5ODT ADP 21.7391
125 5EYK 5U5 22.0339
126 4C2V YJA 22.7273
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