Receptor
PDB id Resolution Class Description Source Keywords
2RDE 1.92 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VCA0042 COMPLEXED WITH C-DI-GMP VIBRIO CHOLERAE C-DI-GMP VIBRIO CHOLERAE VCA0042 STRUCTURAL GENOMICS PSIPROTEIN STRUCTURE INITIATIVE NORTHEAST STRUCTURAL GENOMICSCONSORTIUM NESG UNKNOWN FUNCTION
Ref.: THE STRUCTURAL BASIS OF CYCLIC DIGUANYLATE SIGNAL TRANSDUCTION BY PILZ DOMAINS. EMBO J. V. 26 5153 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C2E A:301;
B:301;
Valid;
Valid;
none;
none;
Kd = 97.1 nM
690.411 C20 H24 N10 O14 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2RDE 1.92 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VCA0042 COMPLEXED WITH C-DI-GMP VIBRIO CHOLERAE C-DI-GMP VIBRIO CHOLERAE VCA0042 STRUCTURAL GENOMICS PSIPROTEIN STRUCTURE INITIATIVE NORTHEAST STRUCTURAL GENOMICSCONSORTIUM NESG UNKNOWN FUNCTION
Ref.: THE STRUCTURAL BASIS OF CYCLIC DIGUANYLATE SIGNAL TRANSDUCTION BY PILZ DOMAINS. EMBO J. V. 26 5153 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 2RDE Kd = 97.1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
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: C2E; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 PCG 1 0.986111
2 35G 1 0.986111
3 C2E 1 1
4 4BW 0.806818 1
5 1YD 0.806818 1
6 5GP 5GP 0.743902 0.958904
7 4UR 0.731959 1
8 6SW 0.627907 0.944444
9 1YC 0.616162 0.972222
10 6J7 0.58427 0.934211
11 2BA 0.534091 0.916667
12 CMP 0.534091 0.902778
13 GMP 0.53012 0.828947
14 1SY 0.495575 1
15 SGP 0.483871 0.825
16 6SZ 0.483871 0.916667
17 3GP 0.478261 0.92
18 1OR 0.474747 0.741176
19 5GP 0.468085 0.933333
20 G 0.468085 0.933333
21 7CH 0.467391 0.888889
22 6SX 0.462366 0.861111
23 6JR 0.457944 0.944444
24 G2R 0.457143 0.886076
25 GPX 0.451923 0.894737
26 GP3 0.44898 0.947368
27 2GP 0.446809 0.907895
28 GDP BEF 0.445545 0.851852
29 GDP 0.444444 0.921053
30 GP2 0.444444 0.886076
31 GNH 0.44 0.909091
32 P2G 0.4375 0.881579
33 G2P 0.436893 0.886076
34 GDP MG 0.435644 0.873418
35 ALF 5GP 0.431373 0.841463
36 GTP 0.431373 0.921053
37 GMV 0.431373 0.897436
38 G1R 0.427184 0.909091
39 GCP 0.427184 0.897436
40 GNP 0.423077 0.897436
41 GSP 0.423077 0.875
42 G3D 0.423077 0.933333
43 GDP AF3 0.420561 0.841463
44 BEF GDP 0.419048 0.841463
45 GTP MG 0.419048 0.873418
46 GCP G 0.415094 0.884615
47 G4P 0.415094 0.933333
48 GAV 0.415094 0.886076
49 P1G 0.414141 0.87013
50 Y9Z 0.410714 0.833333
51 G G 0.409091 0.934211
52 GDP ALF 0.407407 0.841463
53 N6R 0.40708 0.831169
54 N6S 0.40708 0.831169
55 G3A 0.403509 0.947368
56 YGP 0.401786 0.876543
57 G5P 0.4 0.947368
58 0O2 0.4 0.933333
59 GPG 0.4 0.935065
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2RDE; Ligand: C2E; Similar sites found: 86
This union binding pocket(no: 1) in the query (biounit: 2rde.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3IWD M2T 0.005269 0.42646 None
2 3NZ1 3NY 0.005677 0.42206 1.19522
3 4L3L 5FI 0.0002754 0.49839 1.99203
4 3QPB URA 0.004137 0.42866 1.99203
5 1I7M CG 0.005659 0.41992 1.99203
6 2IVD ACJ 0.002607 0.42629 2.39044
7 3KVY URA 0.009798 0.41531 2.39044
8 5H2U 1N1 0.002782 0.40498 2.39044
9 1W8S FBP 0.006392 0.40341 2.39044
10 3TW1 AHN 0.01727 0.40325 2.53165
11 3UW5 MAA CHG PRO 0DQ 0.001663 0.45555 2.58621
12 5FPE 3TR 0.002303 0.46835 2.78884
13 3NKS ACJ 0.0002094 0.45553 2.78884
14 5MX4 HPA 0.007761 0.414 3.00429
15 3LGS ADE 0.001459 0.4561 3.18725
16 1G51 AMP 0.002721 0.44637 3.18725
17 3LGS SAH 0.004283 0.41641 3.18725
18 5LVP ATP 0.007084 0.40637 3.18725
19 5JZJ AN2 0.002504 0.40552 3.18725
20 3UW4 MAA CHG PRO 0DQ 0.006624 0.4252 3.26087
21 4KBA 1QM 0.002466 0.43734 3.58566
22 3JU6 ANP 0.003977 0.43252 3.58566
23 3HAV ATP 0.01791 0.40152 3.58566
24 3CM2 X23 0.002743 0.44053 3.84615
25 3JQ3 ADP 0.004702 0.41903 3.98406
26 3IWJ NAD 0.002043 0.40989 3.98406
27 2GQS C2R 0.00192 0.42406 4.21941
28 5KJW 53C 0.0000009883 0.62104 4.38247
29 1OFL NGK GCD 0.0006113 0.4678 4.38247
30 5DMZ ADP 0.001915 0.40909 4.38247
31 2H8H H8H 0.002415 0.40578 4.38247
32 5C83 4YN 0.002396 0.43795 4.54545
33 1HXD BTN 0.0007145 0.42585 4.78088
34 1M15 ARG 0.0139 0.4195 4.78088
35 1M15 ADP 0.0139 0.4195 4.78088
36 5TVA COA 0.004212 0.40097 5
37 5HV7 RBL 0.0001873 0.45779 5.17928
38 5WZN A2G 0.008755 0.41075 5.17928
39 5XLY C2E 0.00000000008663 0.69734 5.26316
40 4LRJ ANP 0.003068 0.40754 5.32544
41 2YKL NLD 0.005149 0.41273 5.55556
42 4YJK URA 0.0009738 0.46233 5.57769
43 4WOE ADP 0.003384 0.43826 5.57769
44 3H0L ADP 0.003159 0.43215 5.57769
45 4DSU BZI 0.0001047 0.51875 5.82011
46 5IFK HPA 0.005551 0.42677 5.9761
47 1UYY BGC BGC 0.0011 0.46021 6.10687
48 4FFG 0U8 0.01358 0.41103 6.3745
49 2IDO TMP 0.01194 0.41321 6.45161
50 5AOG IAC 0.00001583 0.43997 6.77291
51 5X7Q GLC GLC 0.01658 0.40171 6.77291
52 5HWV MBN 0.003697 0.4341 6.92308
53 3SAO DBH 0.00176 0.45362 7.5
54 5CPR 539 0.006206 0.41798 7.56972
55 2QHV OC9 0.002565 0.43652 7.61905
56 1VMK GUN 0.002675 0.44189 7.96813
57 5F7J ADE 0.001338 0.45813 8.36653
58 3QSB 743 0.006894 0.4112 8.36653
59 3U6W KIV 0.01244 0.40977 8.76494
60 1OSS BEN 0.01771 0.40024 8.96861
61 3CBC DBS 0.001795 0.45888 9.09091
62 3ESS 18N 0.005613 0.42861 9.13043
63 3BJE URA 0.00716 0.42 9.16335
64 4JGT PYR 0.01044 0.40798 9.16335
65 5TVF CGQ 0.009546 0.40893 9.41177
66 1V3S ATP 0.0004669 0.42111 9.48276
67 1FHX 4IP 0.01049 0.4026 10.0775
68 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 0.001142 0.45964 10.5263
69 3EFS BTN 0.001424 0.4078 12.0172
70 5H9P TD2 0.01308 0.40681 12.6582
71 4FE2 AIR 0.002315 0.43351 12.749
72 2WZ5 MET 0.0001289 0.4807 13.0719
73 5H9Y BGC BGC BGC BGC 0.004898 0.40602 13.1474
74 5HES 032 0.01815 0.40056 13.1474
75 3OV6 MK0 0.00004407 0.53915 13.9442
76 2QHS OCA 0.003758 0.42361 15.6118
77 2CJU PHX 0.002676 0.44915 15.7025
78 5FUI APY 0.00003984 0.51615 16.6667
79 5T7I LAT NAG GAL 0.01799 0.40205 16.7742
80 5M6N 7H9 0.0004945 0.48247 17.7966
81 2REG CHT 0.003583 0.43959 17.9283
82 5M6M 7H8 0.00237 0.43817 19.685
83 1SBR VIB 0.002811 0.44 20
84 5CIC 51R 0.01739 0.40116 22.2222
85 4MTI 2DX 0.009389 0.4176 22.6087
86 1HFE CYS 0.00264 0.44277 23.5772
Pocket No.: 2; Query (leader) PDB : 2RDE; Ligand: C2E; 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: 2rde.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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