Receptor
PDB id Resolution Class Description Source Keywords
6BVK 1.8 Å EC: 3.-.-.- RAS:SOS:RAS IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR HOMO SAPIENS RAS SOS INHIBITOR ONCOPROTEIN PROTEIN-PROTEIN COMPLEX MSIGNALING PROTEIN
Ref.: DISCOVERY OF AMINOPIPERIDINE INDOLES THAT ACTIVATE GUANINE NUCLEOTIDE EXCHANGE FACTOR SOS1 AND MODULAT SIGNALING. J. MED. CHEM. 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA C:202;
Part of Protein;
none;
submit data
22.99 Na [Na+]
FMT B:2004;
B:2002;
B:2006;
C:201;
B:2005;
B:2003;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
46.025 C H2 O2 C(=O)...
GNP A:201;
Valid;
none;
submit data
522.196 C10 H17 N6 O13 P3 c1nc2...
MG A:202;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
EAV B:2001;
Valid;
none;
submit data
464.002 C26 H30 Cl N5 O Cc1cc...
GOL B:2007;
B:2008;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6BVK 1.8 Å EC: 3.-.-.- RAS:SOS:RAS IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR HOMO SAPIENS RAS SOS INHIBITOR ONCOPROTEIN PROTEIN-PROTEIN COMPLEX MSIGNALING PROTEIN
Ref.: DISCOVERY OF AMINOPIPERIDINE INDOLES THAT ACTIVATE GUANINE NUCLEOTIDE EXCHANGE FACTOR SOS1 AND MODULAT SIGNALING. J. MED. CHEM. 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 6BVK - 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 209 families.
1 6BVK - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 173 families.
1 6BVK - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
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
Ligand no: 2; Ligand: EAV; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 EAV 1 1
2 EC4 0.822222 0.981818
3 EBY 0.808989 1
4 EAS 0.790698 0.981818
5 EBV 0.459459 0.844828
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6BVK; Ligand: GNP; Similar sites found with APoc: 93
This union binding pocket(no: 1) in the query (biounit: 6bvk.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 2X77 GDP 2.1164
2 3N5C GDP 2.46914
3 5M04 GDP 4.79042
4 4KAX GTP 5.59006
5 4RD0 GDP 5.98802
6 3WY9 GDP 6.45161
7 3WYA GDP 6.45161
8 2HCJ GDP 6.58683
9 3U6B GDP 6.58683
10 2BVN GNP 6.58683
11 1D8T GDP 6.58683
12 5JBQ GDP 6.58683
13 4G5G GDP 6.58683
14 3U6K GDP 6.58683
15 3WXM GTP 6.58683
16 1UPT GTP 6.66667
17 5W7Q GDP 7.18563
18 3CNL GNP 7.18563
19 5W76 GDP 7.18563
20 5W75 GDP 7.18563
21 2C77 GNP 7.90123
22 2C78 GNP 7.90123
23 2RCN GDP 8.38323
24 5EE5 GTP 8.4507
25 4J0Q GDP 9.58084
26 1KK1 GNP 9.58084
27 3DOE GTP 9.69697
28 4P3Y GDP 10.1796
29 5KUT GDP 11.6402
30 1KSH GDP 12.5
31 2XTZ GSP 15.2542
32 4NCN GTP 15.5689
33 5HCN GCP 15.5689
34 4TMZ GSP 15.5689
35 1MKY GDP 16.1677
36 1FQJ ALF 16.6667
37 5CK5 GDP 18.5629
38 2W83 GTP 19.4805
39 2FH5 GTP 23.9521
40 4B47 GDP 28.1437
41 4M9Q GNP 28.7425
42 1YRB GDP 29.3413
43 1R4A GNP 29.4118
44 5YT0 GDP 31.7365
45 5FG3 GDP 31.7365
46 1J2J GTP 31.7365
47 2J59 GTP 31.7365
48 1O3Y GTP 31.7365
49 4DCT GDP 32.3353
50 1ZD9 GDP 32.3353
51 1RE0 GDP 32.3353
52 1S9D GDP 32.3353
53 3AQ4 GDP 32.9341
54 2QN6 GDP 33.3333
55 1YZG GDP 33.5329
56 1ZJ6 G3D 34.1317
57 4ZI2 GNP 40.1198
58 4GOJ GNP 40.1198
59 1FZQ GDP 40.1198
60 5DI3 GNP 41.9162
61 1MR3 G3D 44.3114
62 1GWN GTP 45.509
63 1M7B GTP 45.509
64 3M1I GTP 48.503
65 3GJX GTP 48.503
66 3WYF GTP 48.503
67 3GJ4 GDP 48.503
68 3GJ7 GDP 48.503
69 1Z0J GTP 48.503
70 3WYG GTP 48.503
71 3GJ8 GDP 48.503
72 3GJ5 GDP 48.503
73 1D5C GDP 48.7654
74 4HAT GNP 49.1018
75 5DHF GNP 49.1018
76 6CIT GNP 49.1018
77 5UWQ GNP 49.1018
78 5UWO GNP 49.1018
79 5UWJ GNP 49.1018
80 5UWR GNP 49.1018
81 5UWW GNP 49.1018
82 5UWT GNP 49.1018
83 5UWU GNP 49.1018
84 5UWI GNP 49.1018
85 5UWH GNP 49.1018
86 5UWP GNP 49.1018
87 5DI9 GNP 49.1018
88 5UWS GNP 49.1018
89 3GJ3 GDP 49.1018
90 3CH5 GDP 49.1018
91 1WA5 GTP 49.1018
92 5OEC GDP 49.1018
93 1YVD GNP 49.1124
Pocket No.: 2; Query (leader) PDB : 6BVK; Ligand: EAV; 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: 6bvk.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
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