Receptor
PDB id Resolution Class Description Source Keywords
4ZVF 1.15 Å EC: 2.7.7.65 CRYSTAL STRUCTURE OF GGDEF DOMAIN OF THE E. COLI DOSC - FORM ALPHA-S-BOUND) ESCHERICHIA COLI K-12 OXYGEN SENSING DIGUANYLATE CYCLASE CYCLIC-DI-GMP SIGNALIN
Ref.: STRUCTURAL ANALYSIS OF AN OXYGEN-REGULATED DIGUANYL CYCLASE. ACTA CRYSTALLOGR.,SECT.D V. 71 2158 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:505;
A:504;
 Invalid;
Invalid;
 none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
CA A:503;
A:502;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
40.078 Ca [Ca+2...
GAV A:501;
 Valid;
 none;
 submit data
539.246 C10 H16 N5 O13 P3 S c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4ZVF 1.15 Å EC: 2.7.7.65 CRYSTAL STRUCTURE OF GGDEF DOMAIN OF THE E. COLI DOSC - FORM ALPHA-S-BOUND) ESCHERICHIA COLI K-12 OXYGEN SENSING DIGUANYLATE CYCLASE CYCLIC-DI-GMP SIGNALIN
Ref.: STRUCTURAL ANALYSIS OF AN OXYGEN-REGULATED DIGUANYL CYCLASE. ACTA CRYSTALLOGR.,SECT.D V. 71 2158 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4ZVF - GAV C10 H16 N5 O13 P3 S 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 2 families.
1 4ZVF - GAV C10 H16 N5 O13 P3 S c1nc2c(n1[....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 223 families.
1 4ZVF - GAV C10 H16 N5 O13 P3 S c1nc2c(n1[....
2 4URG - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
3 4URS - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GAV; Similar ligands found: 113
No: Ligand ECFP6 Tc MDL keys Tc
1 GAV 1 1
2 GTP 0.811765 0.961039
3 GDP 0.797619 0.961039
4 GP3 0.764706 0.936709
5 5GP 0.759036 0.948052
6 G 0.759036 0.948052
7 GNH 0.727273 0.948718
8 GSP 0.714286 0.987179
9 GNP 0.714286 0.936709
10 G2P 0.714286 0.925
11 9GM 0.714286 0.936709
12 G1R 0.703297 0.948718
13 GCP 0.703297 0.936709
14 GP2 0.696629 0.925
15 GMV 0.692308 0.936709
16 GDP BEF 0.666667 0.9
17 G2R 0.659794 0.925
18 GTP MG 0.659574 0.923077
19 ALF 5GP 0.655914 0.857143
20 GPG 0.653061 0.925
21 GKE 0.643564 0.925
22 GDC 0.643564 0.925
23 GDD 0.643564 0.925
24 G5P 0.640777 0.936709
25 GTG 0.637255 0.902439
26 GDP AF3 0.632653 0.857143
27 GDP ALF 0.632653 0.857143
28 G3A 0.631068 0.936709
29 6CK 0.631068 0.902439
30 GPD 0.628571 0.891566
31 Y9Z 0.627451 0.870588
32 GMP 0.626506 0.846154
33 GFB 0.621359 0.925
34 GDR 0.621359 0.925
35 0O2 0.62 0.948052
36 GKD 0.619048 0.925
37 YGP 0.617647 0.869048
38 G3D 0.608247 0.948052
39 JB2 0.603774 0.925
40 GDX 0.598131 0.936709
41 G4P 0.59596 0.948052
42 KB7 0.583333 0.797619
43 U2G 0.580357 0.902439
44 GDP 7MG 0.579439 0.878049
45 JB3 0.571429 0.91358
46 CG2 0.570175 0.902439
47 GH3 0.57 0.935897
48 NGD 0.566372 0.925
49 2MD 0.565217 0.904762
50 3GP 0.565217 0.910256
51 ZGP 0.561404 0.882353
52 T99 0.556701 0.923077
53 TAT 0.556701 0.923077
54 FEG 0.552632 0.848837
55 MGD 0.550847 0.904762
56 CAG 0.550847 0.850575
57 DGT 0.55 0.888889
58 PGD 0.545455 0.938272
59 KBD 0.542857 0.797619
60 KBJ 0.537037 0.770115
61 MD1 0.532787 0.904762
62 2GP 0.531915 0.923077
63 GPX 0.528846 0.910256
64 DGI 0.525253 0.888889
65 FE9 0.52459 0.808511
66 TPG 0.524194 0.813187
67 QBQ 0.52 0.948052
68 DBG 0.512 0.91358
69 P2G 0.505155 0.85
70 IDP 0.50505 0.935065
71 BGO 0.5 0.890244
72 MGP 0.5 0.925
73 PGD O 0.496063 0.885057
74 6G0 0.495146 0.925
75 G1R G1R 0.488189 0.890244
76 I2C FE2 CMO CMO 0.488 0.782609
77 AKW 0.487395 0.926829
78 G4M 0.485075 0.850575
79 CZF 0.480392 0.897436
80 P1G 0.48 0.839506
81 DGP 0.479592 0.876543
82 DG 0.479592 0.876543
83 G C 0.47541 0.86747
84 IMP 0.469388 0.922078
85 GGM 0.463415 0.869048
86 G1G 0.456693 0.891566
87 GPC 0.452381 0.848837
88 G7M 0.45 0.9125
89 R7I 0.443396 0.910256
90 R5I 0.443396 0.910256
91 SGP 0.431373 0.864198
92 ATP 0.427184 0.884615
93 HEJ 0.427184 0.884615
94 5FA 0.423077 0.884615
95 AQP 0.423077 0.884615
96 01G 0.422414 0.870588
97 APC G U 0.416667 0.853659
98 GTA 0.416667 0.902439
99 C2E 0.415094 0.886076
100 HFD 0.415094 0.841463
101 PCG 0.415094 0.897436
102 35G 0.415094 0.897436
103 JSQ 0.415094 0.841463
104 6YZ 0.412844 0.8625
105 ADP 0.411765 0.884615
106 5GP 5GP 0.411215 0.85
107 MGQ 0.410714 0.901235
108 AT4 0.407767 0.923077
109 UCG 0.407407 0.878049
110 ITT 0.403846 0.835443
111 G2Q 0.403509 0.925
112 MGO 0.4 0.833333
113 MGV 0.4 0.858824
Similar Ligands (3D)
Ligand no: 1; Ligand: GAV; Similar ligands found: 1
No: Ligand Similarity coefficient
1 ACP 0.8811
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4ZVF; Ligand: GAV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4zvf.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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