Receptor
PDB id Resolution Class Description Source Keywords
6D55 1.68 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 AND STRUCTURE-BASED OPTIMIZATION OF BENZIMIDAZOLE-DERIVED ACTIVATORS OF SOS1-MEDIATED N EXCHANGE ON RAS. J. MED. CHEM. V. 61 8875 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)...
FWA B:2001;
Valid;
none;
submit data
483.024 C26 H32 Cl F N6 Cc1cc...
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...
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
6D55 1.68 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 AND STRUCTURE-BASED OPTIMIZATION OF BENZIMIDAZOLE-DERIVED ACTIVATORS OF SOS1-MEDIATED N EXCHANGE ON RAS. J. MED. CHEM. V. 61 8875 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 283 families.
1 6D55 - FWA C26 H32 Cl F N6 Cc1cc(cc(c....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 235 families.
1 6D55 - FWA C26 H32 Cl F N6 Cc1cc(cc(c....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 193 families.
1 6D55 - FWA C26 H32 Cl F N6 Cc1cc(cc(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FWA; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 FWA 1 1
2 FVM 0.564356 0.8
3 FVG 0.495327 0.826087
4 FVD 0.435185 0.760563
5 FV7 0.435185 0.80597
6 FV4 0.434343 0.80597
7 FVJ 0.431193 0.763889
Ligand no: 2; Ligand: GNP; Similar ligands found: 137
No: Ligand ECFP6 Tc MDL keys Tc
1 9GM 1 1
2 GNP 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 GCP 0.77907 0.948718
8 G1R 0.77907 0.961039
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 GDD 0.690722 0.936709
19 GKE 0.690722 0.936709
20 GDC 0.690722 0.936709
21 G5P 0.686869 0.948718
22 GPG 0.684211 0.936709
23 GFB 0.683673 0.936709
24 GDR 0.683673 0.936709
25 GTG 0.683673 0.91358
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 GDP AF3 0.645833 0.86747
35 GDP ALF 0.645833 0.86747
36 ALF GDP 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 KB7 0.612903 0.807229
46 2MD 0.603604 0.870588
47 CAG 0.60177 0.904762
48 FEG 0.590909 0.858824
49 U2G 0.590909 0.91358
50 GDP 7MG 0.590476 0.888889
51 MGD 0.587719 0.870588
52 G G 0.586538 0.924051
53 ZGP 0.585586 0.848837
54 CG2 0.580357 0.91358
55 KBD 0.568627 0.807229
56 ANP 0.568421 0.922078
57 PGD 0.567797 0.902439
58 MD1 0.567797 0.870588
59 3GP 0.56044 0.922078
60 TPG 0.558333 0.822222
61 GH3 0.55 0.948052
62 KBJ 0.54717 0.77907
63 FE9 0.546219 0.778947
64 GPX 0.539216 0.922078
65 G4M 0.539062 0.860465
66 DGI 0.536082 0.9
67 BGO 0.535088 0.901235
68 IDP 0.53125 0.947368
69 DGT 0.53 0.9
70 2GP 0.526882 0.935065
71 G1R G1R 0.520325 0.901235
72 GCP G 0.518868 0.897436
73 A G 0.516949 0.911392
74 U A G G 0.512605 0.911392
75 AGO 0.504202 0.91358
76 G A A A 0.504202 0.9
77 G1G 0.5 0.902439
78 P2G 0.5 0.860759
79 R7I 0.49505 0.922078
80 R5I 0.49505 0.922078
81 MGP 0.49505 0.936709
82 PGD O 0.492063 0.831461
83 6G0 0.490196 0.936709
84 P1G 0.489796 0.85
85 AKW 0.483051 0.869048
86 DG 0.474227 0.8875
87 DGP 0.474227 0.8875
88 G U 0.466667 0.878049
89 IMP 0.463918 0.934211
90 G2Q 0.462963 0.936709
91 GPC 0.459677 0.858824
92 G C 0.459016 0.878049
93 GTA 0.448276 0.91358
94 G7M 0.444444 0.924051
95 MAP 0.439252 0.898734
96 G G G RPC 0.435484 0.853659
97 ADP 0.434343 0.896104
98 AP5 0.434343 0.871795
99 B4P 0.434343 0.871795
100 A2D 0.43299 0.871795
101 AT4 0.43 0.8625
102 G G G C 0.426357 0.890244
103 AU1 0.425743 0.922078
104 SGP 0.425743 0.807229
105 BA3 0.424242 0.871795
106 C2E 0.423077 0.897436
107 35G 0.423077 0.909091
108 PCG 0.423077 0.909091
109 A G C C 0.423077 0.888889
110 APC G U 0.421875 0.864198
111 HEJ 0.421569 0.896104
112 ATP 0.421569 0.896104
113 5GP 5GP 0.419048 0.860759
114 ACQ 0.419048 0.873418
115 AQP 0.417476 0.896104
116 5FA 0.417476 0.896104
117 01G 0.417391 0.880952
118 AN2 0.415842 0.909091
119 UNP 0.415842 0.810127
120 6AD 0.415094 0.821429
121 M33 0.411765 0.860759
122 ITT 0.411765 0.846154
123 G C C C 0.410448 0.901235
124 JSQ 0.409524 0.851852
125 HFD 0.409524 0.851852
126 G U34 0.408 0.86747
127 ACP 0.407767 0.873418
128 KG4 0.407767 0.873418
129 6YZ 0.407407 0.873418
130 APR 0.403846 0.871795
131 AR6 0.403846 0.871795
132 DG DG 0.403509 0.845238
133 A4P 0.403226 0.848837
134 UCG 0.402985 0.888889
135 AGS 0.4 0.851852
136 SAP 0.4 0.851852
137 AD9 0.4 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6D55; Ligand: FWA; 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: 6d55.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6D55; Ligand: GNP; Similar sites found with APoc: 81
This union binding pocket(no: 2) in the query (biounit: 6d55.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 3N5C GDP 2.46914
2 4KAX GTP 5.59006
3 4RD0 GDP 5.98802
4 3WY9 GDP 6.45161
5 3U6B GDP 6.58683
6 2BVN GNP 6.58683
7 3U6K GDP 6.58683
8 5W76 GDP 7.18563
9 5W75 GDP 7.18563
10 5EE5 GTP 8.4507
11 4J0Q GDP 9.58084
12 4J0Q GDP 9.58084
13 1KK1 GNP 9.58084
14 1SKQ GDP 10.1796
15 4NCN GTP 15.5689
16 4TMZ GSP 15.5689
17 4TMZ GSP 15.5689
18 4NCN GTP 15.5689
19 2AWN ADP 16.1677
20 1FQJ ALF 16.6667
21 5CK5 GDP 18.5629
22 5CK5 GDP 18.5629
23 5CK5 GDP 18.5629
24 2FH5 GTP 23.9521
25 4M9Q GNP 28.7425
26 4M9Q GNP 28.7425
27 1YRB GDP 29.3413
28 1YRB GDP 29.3413
29 5YT0 GDP 31.7365
30 5FG3 GDP 31.7365
31 2J59 GTP 31.7365
32 2J59 GTP 31.7365
33 4DCT GDP 32.3353
34 1RE0 GDP 32.3353
35 4DCT GDP 32.3353
36 2QN6 GDP 33.3333
37 1ZJ6 G3D 34.1317
38 4GOJ GNP 40.1198
39 4ZI2 GNP 40.1198
40 1FZQ GDP 40.1198
41 6IZW GSP 41.3174
42 5DI3 GNP 41.9162
43 5DI3 GNP 41.9162
44 1GWN GTP 45.509
45 1M7B GTP 45.509
46 1GWN GTP 45.509
47 3M1I GTP 48.503
48 3WYF GTP 48.503
49 3GJX GTP 48.503
50 3GJX GTP 48.503
51 3WYF GTP 48.503
52 3WYG GTP 48.503
53 3GJ4 GDP 48.503
54 3GJ7 GDP 48.503
55 1Z0J GTP 48.503
56 3GJ5 GDP 48.503
57 1D5C GDP 48.7654
58 4HAT GNP 49.1018
59 5UWP GNP 49.1018
60 5DHF GNP 49.1018
61 6CIT GNP 49.1018
62 5UWQ GNP 49.1018
63 5UWO GNP 49.1018
64 5UWJ GNP 49.1018
65 5UWR GNP 49.1018
66 5UWW GNP 49.1018
67 5UWU GNP 49.1018
68 5UWT GNP 49.1018
69 5UWI GNP 49.1018
70 5UWS GNP 49.1018
71 1WA5 GTP 49.1018
72 5UWH GNP 49.1018
73 5DI9 GNP 49.1018
74 3CH5 GDP 49.1018
75 1YVD GNP 49.1124
76 6HDU GTP 49.7006
77 6HDU GTP 49.7006
78 6HDU GTP 49.7006
79 6HDU GTP 49.7006
80 6FF8 GTP 49.7006
81 6FF8 GTP 49.7006
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