Receptor
PDB id Resolution Class Description Source Keywords
1ZC3 2 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE RAL-BINDING DOMAIN OF EXO84 IN COMPLEX WITH THE ACTIVE RALA HOMO SAPIENS EXOCYTOSIS SMALL GTPASE GTP-BINDING PROTEIN SIGNALING PROTEIN
Ref.: EXO84 AND SEC5 ARE COMPETITIVE REGULATORY SEC6/8 EFFECTORS TO THE RALA GTPASE. EMBO J. V. 24 2064 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GNP A:700;
C:800;
Valid;
Valid;
none;
none;
submit data
522.196 C10 H17 N6 O13 P3 c1nc2...
MG A:500;
C:600;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ZC3 2 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE RAL-BINDING DOMAIN OF EXO84 IN COMPLEX WITH THE ACTIVE RALA HOMO SAPIENS EXOCYTOSIS SMALL GTPASE GTP-BINDING PROTEIN SIGNALING PROTEIN
Ref.: EXO84 AND SEC5 ARE COMPETITIVE REGULATORY SEC6/8 EFFECTORS TO THE RALA GTPASE. EMBO J. V. 24 2064 2005
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 286 families.
1 1ZC4 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 1ZC3 - GNP C10 H17 N6 O13 P3 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 209 families.
1 1ZC4 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 1ZC3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 3QBT - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
3 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
4 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
5 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
6 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
10 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
11 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
13 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
15 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
18 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
19 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
20 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
22 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
23 3MJH - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
24 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
25 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
26 2CJW Kd = 2.5 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
27 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
28 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
29 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
30 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
31 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
32 3TNF - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
33 1ZC4 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
34 1ZC3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
35 2A9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
36 2A78 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
37 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
38 3TKL - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
40 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
41 1TU3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
42 1UAD Ka = 7260000 M^-1 GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
43 5O74 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
44 3SFV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
45 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
46 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
47 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GNP; Similar ligands found: 132
No: Ligand ECFP6 Tc MDL keys Tc
1 GNP 1 1
2 9GM 1 1
3 GDP 0.839506 0.973684
4 GP3 0.82716 0.948718
5 GTP 0.809524 0.973684
6 GNH 0.807229 0.986842
7 G1R 0.77907 0.961039
8 GCP 0.77907 0.948718
9 GSP 0.770115 0.925
10 5GP 0.756098 0.960526
11 G 0.756098 0.960526
12 G2R 0.747253 0.936709
13 GMV 0.747126 0.948718
14 GAV 0.714286 0.936709
15 GP2 0.712644 0.936709
16 G2P 0.711111 0.936709
17 Y9Z 0.708333 0.880952
18 GDC 0.690722 0.936709
19 GDD 0.690722 0.936709
20 GKE 0.690722 0.936709
21 G5P 0.686869 0.948718
22 GPG 0.684211 0.936709
23 GTG 0.683673 0.91358
24 GDR 0.683673 0.936709
25 GFB 0.683673 0.936709
26 JB2 0.68 0.936709
27 GKD 0.68 0.936709
28 6CK 0.676768 0.91358
29 G3A 0.676768 0.948718
30 GDX 0.673267 0.948718
31 ALF 5GP 0.67033 0.86747
32 YGP 0.663265 0.879518
33 GPD 0.656863 0.902439
34 ALF GDP 0.645833 0.86747
35 GDP AF3 0.645833 0.86747
36 GDP ALF 0.645833 0.86747
37 JB3 0.641509 0.925
38 DBG 0.640351 0.974359
39 G3D 0.638298 0.960526
40 G4P 0.625 0.960526
41 GMP 0.621951 0.857143
42 NGD 0.62037 0.936709
43 GGM 0.618182 0.925926
44 0O2 0.616162 0.960526
45 2MD 0.603604 0.870588
46 CAG 0.60177 0.904762
47 U2G 0.590909 0.91358
48 FEG 0.590909 0.858824
49 GDP 7MG 0.590476 0.888889
50 MGD 0.587719 0.870588
51 G G 0.586538 0.924051
52 ZGP 0.585586 0.848837
53 CG2 0.580357 0.91358
54 ANP 0.568421 0.922078
55 PGD 0.567797 0.902439
56 MD1 0.567797 0.870588
57 3GP 0.56044 0.922078
58 TPG 0.558333 0.822222
59 GH3 0.55 0.948052
60 FE9 0.546219 0.778947
61 GPX 0.539216 0.922078
62 G4M 0.539062 0.860465
63 DGI 0.536082 0.9
64 BGO 0.535088 0.901235
65 IDP 0.53125 0.947368
66 DGT 0.53 0.9
67 2GP 0.526882 0.935065
68 G1R G1R 0.520325 0.901235
69 GCP G 0.518868 0.897436
70 A G 0.516949 0.911392
71 U A G G 0.512605 0.911392
72 G A A A 0.504202 0.9
73 AGO 0.504202 0.91358
74 P2G 0.5 0.860759
75 G1G 0.5 0.902439
76 R7I 0.49505 0.922078
77 MGP 0.49505 0.936709
78 R5I 0.49505 0.922078
79 PGD O 0.492063 0.831461
80 6G0 0.490196 0.936709
81 P1G 0.489796 0.85
82 AKW 0.483051 0.869048
83 DG 0.474227 0.8875
84 DGP 0.474227 0.8875
85 G U 0.466667 0.878049
86 IMP 0.463918 0.934211
87 G2Q 0.462963 0.936709
88 GPC 0.459677 0.858824
89 G C 0.459016 0.878049
90 GTA 0.448276 0.91358
91 G7M 0.444444 0.924051
92 MAP 0.439252 0.898734
93 G G G RPC 0.435484 0.853659
94 B4P 0.434343 0.871795
95 AP5 0.434343 0.871795
96 ADP 0.434343 0.896104
97 A2D 0.43299 0.871795
98 AT4 0.43 0.8625
99 G G G C 0.426357 0.890244
100 AU1 0.425743 0.922078
101 SGP 0.425743 0.807229
102 BA3 0.424242 0.871795
103 A G C C 0.423077 0.888889
104 35G 0.423077 0.909091
105 PCG 0.423077 0.909091
106 C2E 0.423077 0.897436
107 APC G U 0.421875 0.864198
108 HEJ 0.421569 0.896104
109 ATP 0.421569 0.896104
110 ACQ 0.419048 0.873418
111 5GP 5GP 0.419048 0.860759
112 5FA 0.417476 0.896104
113 AQP 0.417476 0.896104
114 01G 0.417391 0.880952
115 AN2 0.415842 0.909091
116 UNP 0.415842 0.810127
117 6AD 0.415094 0.821429
118 M33 0.411765 0.860759
119 ITT 0.411765 0.846154
120 G C C C 0.410448 0.901235
121 HFD 0.409524 0.851852
122 G U34 0.408 0.86747
123 ACP 0.407767 0.873418
124 6YZ 0.407407 0.873418
125 AR6 0.403846 0.871795
126 APR 0.403846 0.871795
127 DG DG 0.403509 0.845238
128 A4P 0.403226 0.848837
129 UCG 0.402985 0.888889
130 SAP 0.4 0.851852
131 AGS 0.4 0.851852
132 AD9 0.4 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ZC3; Ligand: GNP; Similar sites found with APoc: 93
This union binding pocket(no: 1) in the query (biounit: 1zc3.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1UPT GTP None
2 4RD0 GDP 4
3 1KK1 GNP 4.57143
4 3A1S GDP 4.57143
5 3CNL GNP 6.28571
6 2QN6 GDP 6.45161
7 2WJG GDP 7.07965
8 5W7Q GDP 7.9646
9 3WY9 GDP 8.84956
10 5W75 GDP 9.14286
11 5W76 GDP 9.71429
12 4M9Q GNP 9.73451
13 2C77 GNP 10.6195
14 3U6B GDP 11.4286
15 4P3Y GDP 11.4286
16 1D8T GDP 11.4286
17 2BVN GNP 11.4286
18 3U6K GDP 11.4286
19 4J0Q GDP 13.7143
20 4DCT GDP 15.4286
21 6G14 G4P 15.9292
22 4NCN GTP 16.5714
23 4TMZ GSP 16.5714
24 5YT0 GDP 17.7143
25 5FG3 GDP 17.7143
26 2XTZ GSP 18.2857
27 2WIC GNP 20.5993
28 4LC1 GDP 22.2857
29 3EC1 GDP 22.8571
30 4GOJ GNP 25.1429
31 4ZI2 GNP 25.1429
32 1SKQ GDP 26.5487
33 5DI3 GNP 30.2857
34 5KUT GDP 30.2857
35 2X77 GDP 31.4286
36 1YRB GDP 32
37 3CX8 GSP 32.7434
38 1RE0 GDP 33.5366
39 4KAX GTP 35.503
40 3N5C GDP 36.4198
41 1ZJ6 G3D 38.2857
42 1R4A GNP 39.3939
43 1ZD9 GDP 40.5714
44 1A4R GNH 45.1429
45 1A4R GDP 45.1429
46 1GRN GDP 45.7143
47 4YC7 GNP 45.7143
48 1NF3 GNP 46.2857
49 5UPK GNP 46.2857
50 3GJ7 GDP 46.8571
51 3E5H GNP 46.8571
52 3GJ4 GDP 46.8571
53 3GJ5 GDP 46.8571
54 3GJ0 GDP 47.4286
55 3GJ3 GDP 47.4286
56 5DIF GNP 47.4286
57 5UWJ GNP 47.4286
58 5UWP GNP 47.4286
59 4HAT GNP 47.4286
60 5UWI GNP 47.4286
61 5UWW GNP 47.4286
62 5UWR GNP 47.4286
63 5UWQ GNP 47.4286
64 6CIT GNP 47.4286
65 5UWU GNP 47.4286
66 5UWO GNP 47.4286
67 5UWT GNP 47.4286
68 5BXQ GDP 47.4286
69 5DHF GNP 47.4286
70 1WA5 GTP 47.4286
71 5UWH GNP 47.4286
72 5UWS GNP 47.4286
73 1IBR GNP 47.4286
74 5DI9 GNP 47.4286
75 4U5X GNP 47.4286
76 2J0V GDP 48
77 3GJX GTP 48
78 1TX4 ALF GDP 48.5714
79 5HPY GDP 48.5714
80 5JCP GDP ALF 48.5714
81 5IRC GDP 48.5714
82 4XSH GSP 48.5714
83 1CXZ GSP 48.5714
84 3RAB GNP 49.1124
85 3SBD GNP 49.1429
86 4D0N GDP 49.1429
87 6BCB GSP 49.1429
88 6BCA GSP 49.1429
89 2GCO GNP 49.1429
90 3LXR GDP 49.1429
91 4XOI GTP 49.1429
92 1KMQ GNP 49.1429
93 2FJU GSP 49.1429
Pocket No.: 2; Query (leader) PDB : 1ZC3; Ligand: GNP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1zc3.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
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