Receptor
PDB id Resolution Class Description Source Keywords
1UAD 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE RALA-GPPNHP-SEC5 RAL-BINDING DOMAIN COMPLEX HOMO SAPIENS SMALL GTP-BINDING PROTEIN IMMUNOGLOBLIN-LIKE FOLD BETA- SANDWICH ENDOCYTOSIS/EXOCYTOSIS COMPLEX
Ref.: STRUCTURAL BASIS OF THE INTERACTION BETWEEN RALA AND SEC5, A SUBUNIT OF THE SEC6/8 COMPLEX EMBO J. V. 22 3267 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GNP A:200;
B:1200;
Valid;
Valid;
none;
none;
Ka = 7260000 M^-1
522.196 C10 H17 N6 O13 P3 c1nc2...
MG A:300;
B:300;
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
1UAD 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE RALA-GPPNHP-SEC5 RAL-BINDING DOMAIN COMPLEX HOMO SAPIENS SMALL GTP-BINDING PROTEIN IMMUNOGLOBLIN-LIKE FOLD BETA- SANDWICH ENDOCYTOSIS/EXOCYTOSIS COMPLEX
Ref.: STRUCTURAL BASIS OF THE INTERACTION BETWEEN RALA AND SEC5, A SUBUNIT OF THE SEC6/8 COMPLEX EMBO J. V. 22 3267 2003
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 1UAD Ka = 7260000 M^-1 GNP C10 H17 N6 O13 P3 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 1205 families.
1 1UAD Ka = 7260000 M^-1 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 : 1UAD; Ligand: GNP; Similar sites found with APoc: 93
This union binding pocket(no: 1) in the query (biounit: 1uad.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4RD0 GDP 4.0404
2 4B47 GDP 7.07071
3 1KK1 GNP 7.07071
4 2QN6 GDP 7.52688
5 5CK5 GDP 8.08081
6 2C77 GNP 8.08081
7 4M9Q GNP 9.09091
8 3MD0 GDP 9.14286
9 1YRB GDP 10.101
10 2HCJ GDP 11.4286
11 1D8T GDP 11.4286
12 2BVN GNP 11.4286
13 2WJG GDP 12.1212
14 1SKQ GDP 12.5714
15 4DCT GDP 14.8571
16 4LC1 GDP 16
17 4NCN GTP 16.5714
18 5YT0 GDP 17.7143
19 5FG3 GDP 17.7143
20 2RCN GDP 18.1818
21 2XTZ GSP 18.2857
22 5HCN GCP 21.1429
23 2FH5 GTP 28
24 1UPT GTP 28.3333
25 1MR3 G3D 29.7143
26 1FZQ GDP 30.2857
27 5KUT GDP 30.8571
28 1J2J GTP 33.1325
29 1O3Y GTP 33.1325
30 1YZG GDP 33.1429
31 1RE0 GDP 34.1463
32 5M04 GDP 36
33 1MKY GDP 37.1429
34 1ZJ6 G3D 38.8571
35 1R4A GNP 40
36 1ZD9 GDP 41.1429
37 1GWN GTP 42.8571
38 1M7B GTP 42.8571
39 3REF GDP 43.4286
40 1NF3 GNP 45.7143
41 5UPK GNP 45.7143
42 1A4R GNH 45.7143
43 1A4R GDP 45.7143
44 1GRN GDP 46.2857
45 1GRN AF3 46.2857
46 4U5X GNP 46.8571
47 3GJ7 GDP 47.4286
48 3GJ4 GDP 47.4286
49 3GJ8 GDP 47.4286
50 3GJ5 GDP 47.4286
51 4HAT GNP 48
52 5UWU GNP 48
53 5UWQ GNP 48
54 5UWO GNP 48
55 5UWS GNP 48
56 1WA5 GTP 48
57 5UWJ GNP 48
58 5DIF GNP 48
59 5UWI GNP 48
60 5UWW GNP 48
61 5UWR GNP 48
62 5UWT GNP 48
63 6CIT GNP 48
64 5DHF GNP 48
65 5UWH GNP 48
66 1IBR GNP 48
67 5UWP GNP 48
68 5DI9 GNP 48
69 3GJ0 GDP 48
70 3GJ3 GDP 48
71 5BXQ GDP 48
72 3CH5 GDP 48
73 2J0V GDP 48.5714
74 1KMQ GNP 48.5714
75 1E96 GTP 49.1429
76 2W2X GSP 49.1429
77 1CXZ GSP 49.1429
78 1TX4 ALF GDP 49.1429
79 1OW3 GDP 49.1429
80 5IRC GDP 49.1429
81 5HPY GDP 49.1429
82 1MH1 GNP 49.1429
83 3RAB GNP 49.7041
84 1I4D GDP 49.7143
85 3M1I GTP 49.7143
86 3SBD GNP 49.7143
87 1DS6 GDP 49.7143
88 4D0N GDP 49.7143
89 2WKQ GTP 49.7143
90 2GCO GNP 49.7143
91 2FJU GSP 49.7143
92 1HE1 GDP 49.7143
93 2GCN GDP 49.7143
Pocket No.: 2; Query (leader) PDB : 1UAD; 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: 1uad.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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