Receptor
PDB id Resolution Class Description Source Keywords
4U03 2.04 Å EC: 2.7.7.86 STRUCTURE OF THE VIBRIO CHOLERAE DI-NUCLEOTIDE CYCLASE (DNCV COMPLEX WITH GTP AND 5MTHFGLU2 VIBRIO CHOLERAE EL TOR N16961 REGULATION TRANSFERASE
Ref.: STRUCTURAL BIOCHEMISTRY OF A VIBRIO CHOLERAE DINUCL CYCLASE REVEALS CYCLASE ACTIVITY REGULATION BY FOLA MOL.CELL V. 55 931 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TLL A:505;
B:505;
Valid;
Valid;
none;
none;
ic50 = 1.69 uM
588.57 C25 H32 N8 O9 CN1[C...
MG B:504;
A:503;
A:504;
B:503;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
GTP A:501;
B:501;
B:502;
A:502;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
523.18 C10 H16 N5 O14 P3 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4U03 2.04 Å EC: 2.7.7.86 STRUCTURE OF THE VIBRIO CHOLERAE DI-NUCLEOTIDE CYCLASE (DNCV COMPLEX WITH GTP AND 5MTHFGLU2 VIBRIO CHOLERAE EL TOR N16961 REGULATION TRANSFERASE
Ref.: STRUCTURAL BIOCHEMISTRY OF A VIBRIO CHOLERAE DINUCL CYCLASE REVEALS CYCLASE ACTIVITY REGULATION BY FOLA MOL.CELL V. 55 931 2014
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4XJ3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4TY0 - 38V MG n/a n/a
3 4U0M - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
4 4U0N - TLL C25 H32 N8 O9 CN1[C@H](C....
5 4U03 ic50 = 1.69 uM TLL C25 H32 N8 O9 CN1[C@H](C....
6 4XJ4 - 3AT C10 H16 N5 O12 P3 c1nc(c2c(n....
7 4XJ5 - 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 1068 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 922 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: TLL; Similar ligands found: 22
No: Ligand ECFP6 Tc MDL keys Tc
1 TLL 1 1
2 FON 0.663551 0.931507
3 C2F 0.635514 0.972603
4 FFO 0.530435 0.931507
5 THH 0.526316 0.818182
6 THF 0.521739 0.881579
7 MHF 0.521368 0.85
8 DHF 0.495575 0.863014
9 29C 0.483333 0.776316
10 28Z 0.483333 0.776316
11 29D 0.483333 0.776316
12 THG 0.478632 0.863014
13 1YJ 0.478632 0.863014
14 21V 0.445378 0.84
15 DDF 0.445378 0.84
16 LYB 0.442623 0.717949
17 PFG 0.4375 0.779221
18 DZF 0.436975 0.736842
19 FOL 0.436975 0.75
20 9L9 0.410714 0.797297
21 TMF 0.408 0.8125
22 LYA 0.40678 0.705128
Ligand no: 2; Ligand: GTP; Similar ligands found: 147
No: Ligand ECFP6 Tc MDL keys Tc
1 GTP 1 1
2 GP3 0.921053 0.973684
3 GDP 0.909091 1
4 GSP 0.853659 0.948718
5 GNH 0.82716 0.986667
6 G1R 0.819277 0.986667
7 GAV 0.811765 0.961039
8 GNP 0.809524 0.973684
9 GCP 0.797619 0.973684
10 5GP 0.797468 0.986486
11 G 0.797468 0.986486
12 GMV 0.764706 0.973684
13 G2R 0.764045 0.961039
14 G5P 0.755319 0.973684
15 GTG 0.752688 0.936709
16 G2P 0.747126 0.961039
17 G3A 0.744681 0.973684
18 GDD 0.741935 0.961039
19 GKE 0.741935 0.961039
20 GDC 0.741935 0.961039
21 0O2 0.736264 0.986486
22 GP2 0.729412 0.961039
23 6CK 0.726316 0.936709
24 Y9Z 0.723404 0.902439
25 GPG 0.717391 0.961039
26 GFB 0.715789 0.961039
27 GDR 0.715789 0.961039
28 GDP MG 0.712644 0.923077
29 GDP BEF 0.704545 0.9
30 GPD 0.704082 0.925
31 JB2 0.693878 0.961039
32 GKD 0.693878 0.961039
33 GCP G 0.692308 0.935065
34 GDX 0.686869 0.973684
35 ALF 5GP 0.685393 0.888889
36 GTP MG 0.681319 0.923077
37 BEF GDP 0.681319 0.888889
38 GH3 0.681319 0.973333
39 YGP 0.677083 0.901235
40 G3D 0.67033 0.986486
41 GDP AF3 0.659574 0.888889
42 GDP ALF 0.659574 0.888889
43 DGT 0.659341 0.923077
44 GMP 0.658228 0.88
45 G4P 0.655914 0.986486
46 JB3 0.653846 0.948718
47 NGD 0.647619 0.961039
48 CAG 0.642202 0.880952
49 2MD 0.62963 0.891566
50 G G 0.622449 0.935065
51 MGP 0.619565 0.961039
52 U2G 0.616822 0.936709
53 6G0 0.612903 0.961039
54 MGD 0.612613 0.891566
55 TPG 0.608696 0.840909
56 CG2 0.605505 0.936709
57 GDP 7MG 0.601942 0.911392
58 FEG 0.601852 0.879518
59 ZGP 0.59633 0.869048
60 MD1 0.591304 0.891566
61 PGD 0.591304 0.925
62 3GP 0.590909 0.946667
63 GPX 0.581633 0.946667
64 DGI 0.580645 0.923077
65 IDP 0.576087 0.972973
66 DBG 0.567797 0.948718
67 FE9 0.555556 0.776596
68 2GP 0.555556 0.96
69 G4M 0.547619 0.880952
70 BGO 0.544643 0.924051
71 I2C FE2 CMO CMO 0.538462 0.808989
72 ATP 0.537634 0.92
73 G1G 0.533898 0.925
74 AQP 0.531915 0.92
75 5FA 0.531915 0.92
76 G A A A 0.525862 0.923077
77 U A G G 0.521368 0.935065
78 01G 0.518868 0.902439
79 ITT 0.510638 0.868421
80 P2G 0.510638 0.883117
81 GGM 0.504274 0.901235
82 G1R G1R 0.504065 0.924051
83 DGP 0.5 0.910256
84 PGD O 0.5 0.850575
85 MGO 0.5 0.864198
86 P1G 0.5 0.871795
87 DG 0.5 0.910256
88 GTA 0.495495 0.936709
89 B4P 0.489362 0.894737
90 AP5 0.489362 0.894737
91 IMP 0.489362 0.959459
92 7DT 0.484536 0.906667
93 G G U 0.482143 0.935065
94 GPC 0.479339 0.879518
95 G C 0.478992 0.9
96 BA3 0.478723 0.894737
97 ADP 0.473684 0.92
98 G2Q 0.471698 0.961039
99 G7M 0.46875 0.948052
100 25L 0.458716 0.907895
101 A2D 0.457447 0.894737
102 RGT 0.45045 0.909091
103 AGS 0.45 0.873418
104 SAP 0.45 0.873418
105 SGP 0.44898 0.82716
106 U G A 0.448529 0.888889
107 A4P 0.445378 0.869048
108 G G G RPC 0.442623 0.875
109 ACQ 0.441176 0.896104
110 ANP 0.441176 0.896104
111 8GT 0.441176 0.875
112 APC G U 0.44 0.886076
113 G U34 0.438017 0.888889
114 6AD 0.436893 0.841463
115 G G G C 0.433071 0.9125
116 UP5 0.432203 0.873418
117 35G 0.431373 0.933333
118 C2E 0.431373 0.921053
119 PCG 0.431373 0.933333
120 A G C C 0.429688 0.911392
121 5GP 5GP 0.427184 0.883117
122 TAT 0.427184 0.884615
123 APR 0.425743 0.894737
124 AR6 0.425743 0.894737
125 AN2 0.424242 0.907895
126 7DD 0.424242 0.906667
127 DG DG 0.423423 0.865854
128 AD9 0.421569 0.896104
129 M33 0.42 0.883117
130 7D4 0.42 0.835443
131 UCG 0.419847 0.911392
132 H6Y 0.419048 0.946667
133 G C C C 0.416667 0.924051
134 ACP 0.415842 0.896104
135 T5A 0.414634 0.802326
136 MGQ 0.412844 0.935897
137 ADQ 0.412844 0.871795
138 A1R 0.412844 0.839506
139 MGT 0.411215 0.823529
140 A G U 0.410072 0.888889
141 93A 0.41 0.833333
142 A22 0.407407 0.907895
143 CA0 0.405941 0.896104
144 ATF 0.40566 0.884615
145 AGO 0.404762 0.888889
146 MGV 0.401786 0.890244
147 CGP 0.4 0.86747
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4U03; Ligand: GTP; Similar sites found: 6
This union binding pocket(no: 1) in the query (biounit: 4u03.bio1) has 54 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5C3R AKG 0.03579 0.40622 2.62391
2 5C3R HMU 0.03579 0.40622 2.62391
3 2ZHL NAG GAL GAL NAG 0.03972 0.41304 3.37838
4 3P7N FMN 0.02219 0.41363 5.03876
5 3JYY PPV 0.008601 0.46122 5.22648
6 1GEG GLC 0.02354 0.44209 7.42188
Pocket No.: 2; Query (leader) PDB : 4U03; Ligand: GTP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4u03.bio1) has 54 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4U03; Ligand: TLL; Similar sites found: 6
This union binding pocket(no: 3) in the query (biounit: 4u03.bio1) has 54 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5C3R HMU 0.03579 0.40622 2.62391
2 5C3R AKG 0.03579 0.40622 2.62391
3 2ZHL NAG GAL GAL NAG 0.03972 0.41304 3.37838
4 3P7N FMN 0.02219 0.41363 5.03876
5 3JYY PPV 0.008601 0.46122 5.22648
6 1GEG GLC 0.02354 0.44209 7.42188
Pocket No.: 4; Query (leader) PDB : 4U03; Ligand: GTP; 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: 4u03.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4U03; Ligand: TLL; Similar sites found: 14
This union binding pocket(no: 5) in the query (biounit: 4u03.bio2) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4COQ SAN 0.0406 0.41779 2.02429
2 4KBA 1QM 0.03199 0.41947 2.41692
3 1B74 DGN 0.02639 0.42695 2.75591
4 2OFD NGA 0.03371 0.42136 2.8169
5 2XG5 EC2 0.01231 0.46325 4.04624
6 2XG5 EC5 0.01231 0.46325 4.04624
7 4N14 WR7 0.02871 0.42237 6.36943
8 3I7V B4P 0.002208 0.4093 8.20895
9 3SJK LYS PRO VAL LEU ARG THR ALA 0.04161 0.41836 10.5263
10 2QQD AG2 0.04857 0.41323 10.7143
11 4I67 G G G RPC 0.03226 0.41555 12.6437
12 1RL4 BL5 0.04376 0.42139 13.8298
13 2VWA PTY 0.04016 0.42654 13.8614
14 4LO2 GAL BGC 0.04918 0.40219 14.966
Pocket No.: 6; Query (leader) PDB : 4U03; Ligand: GTP; Similar sites found: 13
This union binding pocket(no: 6) in the query (biounit: 4u03.bio2) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2B56 U5P 0.001565 0.40833 1.87354
2 2B56 UTP 0.001565 0.40833 1.87354
3 5W0N 2KH 0.000033 0.43362 2.48139
4 5A2Z GTP 0.00004866 0.40384 2.8103
5 2Q0D ATP 0.000007177 0.50934 2.83286
6 3HJ1 UTP 0.0002213 0.4032 3.35917
7 3HIY UTP 0.00007959 0.41255 3.38542
8 3PUR 2HG 0.02679 0.41233 3.74707
9 4NKT 2KH 0.00009288 0.40952 7.03812
10 5AIG VPR 0.02219 0.40707 8
11 1EPB REA 0.01486 0.40481 8.53659
12 4JH6 FCN 0.0107 0.42737 10.8696
13 1W6P NDG GAL 0.02415 0.41536 14.1791
Feedback