Receptor
PDB id Resolution Class Description Source Keywords
3KYG 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VCA0042 (L135R) COMPLEXED WITH C-DI-GMP VIBRIO CHOLERAE C-DI-GMP PILZ DOMAIN PP4397 VCA0042 UNKNOWN FUNCTION
Ref.: STRUCTURE OF PP4397 REVEALS THE MOLECULAR BASIS FOR DIFFERENT C-DI-GMP BINDING MODES BY PILZ DOMAIN PROTEINS. J.MOL.BIOL. V. 398 97 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP 5GP A:501;
A:503;
B:501;
B:503;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 55.1 nM
688.4 n/a [P+]1...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KYG 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VCA0042 (L135R) COMPLEXED WITH C-DI-GMP VIBRIO CHOLERAE C-DI-GMP PILZ DOMAIN PP4397 VCA0042 UNKNOWN FUNCTION
Ref.: STRUCTURE OF PP4397 REVEALS THE MOLECULAR BASIS FOR DIFFERENT C-DI-GMP BINDING MODES BY PILZ DOMAIN PROTEINS. J.MOL.BIOL. V. 398 97 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
2 2RDE Kd = 97.1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
2 2RDE Kd = 97.1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP 5GP; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 5GP 1 1
2 35G 0.743902 0.945205
3 PCG 0.743902 0.945205
4 C2E 0.743902 0.958904
5 1YD 0.632653 0.958904
6 4BW 0.632653 0.958904
7 4UR 0.579439 0.958904
8 GMP 0.52381 0.815789
9 1YC 0.518868 0.931507
10 3GP 0.473118 0.906667
11 SGP 0.463158 0.8125
12 G 0.463158 0.894737
13 5GP 0.463158 0.894737
14 GDP BEF 0.455446 0.8625
15 GDP 0.454545 0.883117
16 6SW 0.453608 0.90411
17 G1R 0.45098 0.871795
18 GDP MG 0.445545 0.884615
19 GP3 0.444444 0.909091
20 2GP 0.442105 0.87013
21 ALF 5GP 0.441176 0.851852
22 GP2 0.44 0.85
23 G2R 0.439252 0.85
24 GNH 0.435644 0.871795
25 6J7 0.434343 0.896104
26 P2G 0.43299 0.868421
27 G3D 0.432692 0.894737
28 G2P 0.432692 0.85
29 GTP MG 0.428571 0.884615
30 BEF GDP 0.428571 0.851852
31 GMV 0.427184 0.860759
32 GTP 0.427184 0.883117
33 GCP G 0.424528 0.896104
34 G4P 0.424528 0.894737
35 GCP 0.423077 0.860759
36 GPX 0.420561 0.857143
37 GSP 0.419048 0.839506
38 GNP 0.419048 0.860759
39 G G 0.418182 0.946667
40 GDP AF3 0.416667 0.851852
41 GDP ALF 0.416667 0.851852
42 GAV 0.411215 0.85
43 P1G 0.41 0.857143
44 Y9Z 0.40708 0.8
45 G G U 0.405172 0.946667
46 GH3 0.401869 0.883117
47 G3A 0.4 0.909091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KYG; Ligand: 5GP 5GP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3kyg.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3KYG; Ligand: 5GP 5GP; 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: 3kyg.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3KYG; Ligand: 5GP 5GP; Similar sites found: 81
This union binding pocket(no: 3) in the query (biounit: 3kyg.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4TWP AXI 0.04237 0.40417 1.32159
2 5DQ8 FLF 0.013 0.40357 1.32159
3 3G5D 1N1 0.009922 0.42918 1.76211
4 5H2U 1N1 0.003282 0.40935 1.76211
5 3EM0 CHD 0.008879 0.42836 2.17391
6 4L3L 5FI 0.001013 0.45227 2.20264
7 5EW9 5VC 0.01466 0.44194 2.20264
8 3GC8 B45 0.003688 0.4177 2.20264
9 3IES M24 0.0187 0.40095 2.20264
10 4GID 0GH 0.00397 0.46976 2.64317
11 2X4Z X4Z 0.002538 0.43964 2.64317
12 3I9U DTU 0.01369 0.4214 2.64317
13 5HCY 60D 0.01505 0.41226 2.64317
14 4MIB 28M 0.03818 0.40871 2.64317
15 2YAK OSV 0.009487 0.40849 2.64317
16 5EOB 5QQ 0.03173 0.40395 2.64317
17 4LOO SB4 0.005334 0.40075 2.64317
18 2X32 OTP 0.03036 0.40033 2.7933
19 2GU8 796 0.0007417 0.4835 3.0837
20 3NKS ACJ 0.0004515 0.46068 3.0837
21 3KRR DQX 0.0036 0.45572 3.0837
22 3SXF BK5 0.01165 0.40933 3.0837
23 5VC5 96M 0.008388 0.40817 3.0837
24 3EEL 53T 0.02335 0.40234 3.0837
25 5UIU 8CG 0.01333 0.40181 3.0837
26 5KJW 53C 0.000001045 0.4651 3.52423
27 3QCQ 3Q0 0.01498 0.43551 3.52423
28 4ZUL UN1 0.01284 0.41365 3.52423
29 4DQ2 BTX 0.009129 0.40925 3.52423
30 3E9I XAH 0.01199 0.4039 3.52423
31 3RG9 NDP 0.007269 0.42101 3.96476
32 5F3I 5UJ 0.02552 0.40927 3.96476
33 5DEY 59T 0.02892 0.40519 3.96476
34 2Z9I GLY ALA THR VAL 0.02077 0.41294 4.32099
35 4WHZ 3NL 0.004291 0.4417 4.40529
36 3IWJ NAD 0.004425 0.40396 4.40529
37 2IU8 PLM 0.003193 0.40298 4.40529
38 3ZJX BOG 0.01079 0.4221 4.84582
39 3VZ3 NAP 0.006571 0.41829 4.84582
40 5UKL SIX 0.005961 0.41481 4.84582
41 1HXD BTN 0.004208 0.41159 4.84582
42 3A5Z KAA 0.01005 0.40735 5.2356
43 4CS4 ANP 0.00701 0.4239 5.28634
44 5FKP 6UL 0.006891 0.4134 5.28634
45 3G08 FEE 0.03084 0.40526 5.28634
46 5BVE 4VG 0.002775 0.45979 5.72687
47 4LH0 GLV 0.01885 0.40288 5.72687
48 4DSU BZI 0.000103 0.40486 5.82011
49 1ZB6 GST 0.002316 0.4361 6.1674
50 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.0267 0.40901 6.1674
51 2JDR L20 0.0267 0.40901 6.1674
52 3MVH WFE 0.01349 0.40158 6.1674
53 1B7Y FYA 0.01106 0.40138 6.1674
54 4XTX 590 0.00792 0.41334 6.2963
55 2WLG SOP 0.01013 0.428 6.97674
56 5A89 FMN 0.01304 0.41612 7.05128
57 4CLI 5P8 0.00948 0.42174 7.48899
58 2XG5 EC2 0.01969 0.40116 7.51445
59 2XG5 EC5 0.01969 0.40116 7.51445
60 5W4W 9WG 0.00592 0.41774 9.2511
61 4KBA 1QM 0.01051 0.40378 9.2511
62 1V3S ATP 0.002462 0.42165 9.48276
63 5XDT ZI7 0.008415 0.40811 9.69163
64 4YSW NAI 0.03151 0.40749 10.1322
65 5LYH 7B8 0.01247 0.40561 10.3627
66 3EFS BTN 0.004276 0.40936 10.7296
67 3OV6 MK0 0.0001008 0.49899 11.0132
68 1LSH PLD 0.005491 0.41921 12.7753
69 4LAE NAP 0.03483 0.40125 13.1737
70 4LAE 1VM 0.03483 0.40125 13.1737
71 3RUG DB6 0.008389 0.42785 13.2159
72 5XLY C2E 0.000000001196 0.67759 14.2857
73 2CJU PHX 0.004225 0.44749 15.7025
74 1VJY 460 0.005611 0.42141 17.1806
75 1WZ1 DNS 0.0168 0.41164 17.6991
76 5LRT ADP 0.006186 0.41109 20.2643
77 4X6F 3XU 0.00104 0.46352 23.8095
78 4WO4 JLS 0.00007861 0.51696 25
79 5U98 1KX 0.01001 0.43191 25.2525
80 5L2J 6UL 0.001749 0.47251 25.5102
81 5L2J 70E 0.001867 0.47251 25.5102
Pocket No.: 4; Query (leader) PDB : 3KYG; Ligand: 5GP 5GP; Similar sites found: 58
This union binding pocket(no: 4) in the query (biounit: 3kyg.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BL9 CP6 0.01105 0.42036 1.32159
2 2BL9 NDP 0.01105 0.42036 1.32159
3 4WUP 3UF 0.04557 0.40103 1.32159
4 3C6K MTA 0.02448 0.40359 1.76211
5 3C6K SPD 0.02448 0.40359 1.76211
6 4IEN GDP 0.008885 0.40063 1.84049
7 2QIA U20 0.002332 0.45056 2.20264
8 2C49 ADN 0.007819 0.40312 2.20264
9 4O9S 2RY 0.007546 0.41578 2.32558
10 1OUK 084 0.002383 0.49054 2.64317
11 1MO9 FAD 0.017 0.43804 2.64317
12 1MO9 KPC 0.02008 0.43473 2.64317
13 3UDZ ADP 0.005484 0.41199 2.64317
14 5MW4 5JU 0.02358 0.40818 2.64317
15 3LAD FAD 0.01332 0.42221 3.0837
16 1RE8 BD2 0.01917 0.41527 3.0837
17 2IVD ACJ 0.002139 0.41443 3.0837
18 3ORK AGS 0.007989 0.41313 3.0837
19 4WB6 ATP 0.01578 0.40086 3.0837
20 3HAZ NAD 0.02074 0.40048 3.0837
21 4QMN DB8 0.01333 0.41426 3.22581
22 1KRR ACO 0.01647 0.40271 3.44828
23 4I3V NAD 0.01341 0.42116 3.52423
24 5F7J ADE 0.008368 0.40558 3.52423
25 5C5H 4YB 0.01518 0.40304 3.52423
26 3RG9 WRA 0.004258 0.44252 3.96476
27 5A3T MMK 0.01519 0.40691 3.96476
28 3IA4 NDP 0.02133 0.40108 4.32099
29 2XVD AS6 0.007016 0.42012 4.40529
30 4NV7 COA 0.008422 0.41357 4.40529
31 4WNK 453 0.01086 0.41254 4.40529
32 5LJB RTL 0.00666 0.41007 4.44444
33 4QYN RTL 0.009131 0.40729 4.51128
34 2GQS C2R 0.003363 0.41173 4.84582
35 4B0T ADP 0.01012 0.40837 4.84582
36 4MOB ADP 0.001381 0.40526 4.84582
37 3IX8 TX3 0.01518 0.40021 5.20231
38 2QHV OC9 0.002625 0.44076 5.2381
39 4CS4 AXZ 0.005618 0.44159 5.28634
40 1E1O LYS 0.01618 0.40037 5.28634
41 4LRJ ANP 0.004315 0.41254 5.32544
42 4CQE CQE 0.005281 0.43584 5.72687
43 5U3F 7TS 0.005844 0.41444 5.72687
44 4XV1 904 0.01289 0.4127 5.72687
45 2XIQ MLC 0.01858 0.40152 5.72687
46 1UYY BGC BGC 0.001029 0.40312 6.10687
47 2OFV 242 0.00611 0.43054 6.1674
48 3LVW GSH 0.01827 0.40874 6.60793
49 5A89 ADP 0.02272 0.40987 7.05128
50 5TA6 79D 0.008572 0.41465 7.92952
51 3LXK MI1 0.01367 0.40518 7.92952
52 1RM6 PCD 0.01758 0.41446 8.81057
53 4ANW O92 0.01979 0.40265 8.81057
54 4NG2 OHN 0.01245 0.40421 9.73451
55 5M6N 7H9 0.001426 0.40024 10.1695
56 2JLD AG1 0.01193 0.41431 10.5727
57 3H0L ADP 0.001829 0.40616 10.5727
58 2F5Z FAD 0.02737 0.40758 17.1875
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