Receptor
PDB id Resolution Class Description Source Keywords
3KUD 2.15 Å EC: 2.7.11.1 COMPLEX OF RAS-GDP WITH RAFRBD(A85K) HOMO SAPIENS RAS-EFFECTOR COMPLEX GTP-BINDING NUCLEOTIDE-BINDING PROTOONCOGENE TRANSFERASE GTP BINDING PROTEIN-TRANSFERASE COMP
Ref.: WHAT MAKES RAS AN EFFICIENT MOLECULAR SWITCH: A COMPUTATIONAL, BIOPHYSICAL, AND STRUCTURAL STUDY OF INTERACTIONS WITH MUTANTS OF RAF. J.MOL.BIOL. V. 399 422 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:170;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:171;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KUD 2.15 Å EC: 2.7.11.1 COMPLEX OF RAS-GDP WITH RAFRBD(A85K) HOMO SAPIENS RAS-EFFECTOR COMPLEX GTP-BINDING NUCLEOTIDE-BINDING PROTOONCOGENE TRANSFERASE GTP BINDING PROTEIN-TRANSFERASE COMP
Ref.: WHAT MAKES RAS AN EFFICIENT MOLECULAR SWITCH: A COMPUTATIONAL, BIOPHYSICAL, AND STRUCTURAL STUDY OF INTERACTIONS WITH MUTANTS OF RAF. J.MOL.BIOL. V. 399 422 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 125 families.
1 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
2 6EPO - BPW C9 H12 Cl N c1cc(ccc1C....
3 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
4 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
5 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
6 6H46 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 6EPP - BOQ C12 H19 N O3 CCOC(=O)c1....
8 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
10 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 6EPN - BQ2 C11 H13 N O2 c1ccc2c(c1....
12 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
13 6GQX - F8K C23 H27 N2 O2 C[NH+](C)C....
14 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
15 6EPM - BQ5 C13 H15 N3 c1ccc(cc1)....
16 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
17 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
19 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
21 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
22 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
23 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
24 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
25 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
26 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
27 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
28 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
29 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
30 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
31 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
32 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
33 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
34 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
35 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
36 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 63 families.
1 1GUA Kd = 40 nM GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 168
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 GNP 0.839506 0.973684
6 9GM 0.839506 0.973684
7 G 0.828947 0.986486
8 5GP 0.828947 0.986486
9 G1R 0.82716 0.986667
10 GCP 0.82716 0.973684
11 GSP 0.817073 0.948718
12 GAV 0.797619 0.961039
13 GMV 0.792683 0.973684
14 G2P 0.77381 0.961039
15 G2R 0.770115 0.961039
16 GP2 0.756098 0.961039
17 GKE 0.747253 0.961039
18 GDD 0.747253 0.961039
19 GDC 0.747253 0.961039
20 GPG 0.741573 0.961039
21 G3D 0.732558 0.986486
22 ALF 5GP 0.729412 0.888889
23 Y9Z 0.728261 0.902439
24 G5P 0.723404 0.973684
25 GDR 0.72043 0.961039
26 GFB 0.72043 0.961039
27 GTG 0.72043 0.936709
28 G4P 0.715909 0.986486
29 6CK 0.712766 0.936709
30 G3A 0.712766 0.973684
31 GDP AF3 0.7 0.888889
32 GDP ALF 0.7 0.888889
33 ALF GDP 0.7 0.888889
34 YGP 0.698925 0.901235
35 JB2 0.697917 0.961039
36 GKD 0.697917 0.961039
37 GPD 0.690722 0.925
38 GDX 0.690722 0.973684
39 GMP 0.684211 0.88
40 0O2 0.666667 0.986486
41 JB3 0.656863 0.948718
42 NGD 0.650485 0.961039
43 GDP 7MG 0.636364 0.911392
44 DGI 0.636364 0.923077
45 U2G 0.634615 0.936709
46 GPX 0.634409 0.946667
47 G G 0.632653 0.948052
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 KB7 0.629214 0.82716
52 CG2 0.622642 0.936709
53 FEG 0.619048 0.879518
54 MGD 0.614679 0.891566
55 ZGP 0.613208 0.869048
56 GH3 0.612903 0.973333
57 3GP 0.611765 0.946667
58 MD1 0.607143 0.891566
59 PGD 0.59292 0.925
60 DGT 0.591398 0.923077
61 BGO 0.588785 0.924051
62 TPG 0.582609 0.840909
63 DBG 0.582609 0.948718
64 KBD 0.581633 0.82716
65 2GP 0.574713 0.96
66 FE9 0.570175 0.776596
67 GCP G 0.56 0.921053
68 KBJ 0.558824 0.797619
69 G A A A 0.553571 0.923077
70 A G 0.553571 0.935065
71 MGP 0.553191 0.961039
72 U A G G 0.548673 0.935065
73 G4M 0.548387 0.880952
74 6G0 0.547368 0.961039
75 G1R G1R 0.542373 0.924051
76 P2G 0.527473 0.883117
77 PGD O 0.525 0.850575
78 ADP 0.522222 0.92
79 R5I 0.520833 0.946667
80 R7I 0.520833 0.946667
81 GGM 0.517544 0.901235
82 DGP 0.516484 0.910256
83 DG 0.516484 0.910256
84 P1G 0.516129 0.871795
85 G U 0.513274 0.9
86 G1G 0.508475 0.925
87 IMP 0.505495 0.959459
88 AKW 0.504425 0.890244
89 G C 0.504348 0.9
90 GPC 0.491525 0.879518
91 G7M 0.483871 0.948052
92 6AD 0.479592 0.841463
93 ATP 0.473684 0.92
94 HEJ 0.473684 0.92
95 G2Q 0.471154 0.961039
96 AQP 0.46875 0.92
97 5FA 0.46875 0.92
98 GTA 0.468468 0.936709
99 7DD 0.468085 0.906667
100 G G G RPC 0.466102 0.875
101 SGP 0.463158 0.82716
102 01G 0.462963 0.902439
103 JSQ 0.459184 0.873418
104 HFD 0.459184 0.873418
105 AP5 0.457447 0.894737
106 B4P 0.457447 0.894737
107 A2D 0.456522 0.894737
108 6YZ 0.455446 0.896104
109 G G G C 0.455285 0.9125
110 ANP 0.454545 0.896104
111 5GP 5GP 0.454545 0.883117
112 ACQ 0.454545 0.896104
113 AT4 0.452632 0.884615
114 A G C C 0.451613 0.911392
115 APC G U 0.45082 0.886076
116 PRT 0.449541 0.959459
117 G U34 0.449153 0.888889
118 DG DG 0.448598 0.865854
119 ITT 0.447917 0.868421
120 BA3 0.446809 0.894737
121 35G 0.444444 0.933333
122 PCG 0.444444 0.933333
123 C2E 0.444444 0.921053
124 MGO 0.441176 0.864198
125 AN2 0.4375 0.907895
126 G C C C 0.4375 0.924051
127 NO7 0.436893 0.860759
128 M33 0.43299 0.883117
129 UCG 0.429688 0.911392
130 A G U 0.42963 0.888889
131 ACP 0.428571 0.896104
132 MGQ 0.424528 0.935897
133 7DT 0.424242 0.906667
134 APR 0.424242 0.894737
135 AR6 0.424242 0.894737
136 93A 0.42268 0.833333
137 A4P 0.420168 0.869048
138 AGS 0.42 0.873418
139 AD9 0.42 0.896104
140 G8D 0.42 0.875
141 SAP 0.42 0.873418
142 CA0 0.418367 0.896104
143 ATF 0.417476 0.884615
144 AGO 0.414634 0.888889
145 A G U U 0.414286 0.888889
146 KG4 0.414141 0.896104
147 NIA 0.413043 0.82716
148 MGV 0.412844 0.890244
149 T99 0.411765 0.884615
150 TAT 0.411765 0.884615
151 A1R 0.411215 0.839506
152 ADQ 0.411215 0.871795
153 RGT 0.410714 0.909091
154 CGP 0.409836 0.86747
155 HQG 0.409524 0.907895
156 C1Z 0.409091 0.986486
157 AMP 0.408602 0.893333
158 A 0.408602 0.893333
159 UP5 0.40678 0.873418
160 C2R 0.406593 0.906667
161 AMZ 0.406593 0.918919
162 JBT 0.405882 0.778947
163 A22 0.40566 0.907895
164 25L 0.405405 0.907895
165 ADX 0.40404 0.809524
166 8OD 0.401961 0.946667
167 4TC 0.4 0.851852
168 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KUD; Ligand: GDP; Similar sites found with APoc: 68
This union binding pocket(no: 1) in the query (biounit: 3kud.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5KUT GDP 6.34921
2 3U6B GDP 6.62651
3 3U6K GDP 6.62651
4 5W7Q GDP 7.22892
5 5W76 GDP 7.22892
6 5W75 GDP 7.22892
7 3WY9 GDP 7.40741
8 4LC1 GDP 8.64198
9 3N5C GDP 8.64198
10 4LC1 GDP 8.64198
11 1KK1 GNP 9.63855
12 4J0Q GDP 9.87654
13 4J0Q GDP 9.87654
14 1SKQ GDP 10.241
15 2WJG GDP 12.0482
16 5CK5 GDP 18.6747
17 5CK5 GDP 18.6747
18 5CK5 GDP 18.6747
19 2FH5 GTP 23.494
20 2FH5 GTP 23.494
21 2FH5 GTP 23.494
22 1YRB GDP 29.5181
23 1YRB GDP 29.5181
24 5YT0 GDP 31.9277
25 5FG3 GDP 31.9277
26 4DCT GDP 32.5301
27 1ZD9 GDP 32.5301
28 1RE0 GDP 32.5301
29 2QN6 GDP 33.3333
30 1ZJ6 G3D 34.3373
31 1FZQ GDP 40.3614
32 1D5C GDP 48.7654
33 3WYF GTP 48.7952
34 3M1I GTP 48.7952
35 3RAB GNP 48.7952
36 3GJX GTP 48.7952
37 3WYF GTP 48.7952
38 1Z0J GTP 48.7952
39 3WYG GTP 48.7952
40 3GJ4 GDP 48.7952
41 3GJ7 GDP 48.7952
42 3GJ5 GDP 48.7952
43 3GJX GTP 48.7952
44 1IBR GNP 49.3976
45 4HAT GNP 49.3976
46 5UWP GNP 49.3976
47 5UWQ GNP 49.3976
48 5UWW GNP 49.3976
49 6CIT GNP 49.3976
50 5UWU GNP 49.3976
51 5UWI GNP 49.3976
52 5UWO GNP 49.3976
53 5DHF GNP 49.3976
54 5UWT GNP 49.3976
55 1WA5 GTP 49.3976
56 5UWH GNP 49.3976
57 5UWS GNP 49.3976
58 5BXQ GDP 49.3976
59 5BXQ GDP 49.3976
60 3GJ3 GDP 49.3976
61 1YVD GNP 49.3976
62 5BXQ GDP 49.3976
63 3CH5 GDP 49.3976
64 1IBR GNP 49.3976
65 5UWJ GNP 49.3976
66 5UWR GNP 49.3976
67 5DI9 GNP 49.3976
68 5OEC GDP 49.3976
69 6HDU GTP 50
70 6HDU GTP 50
71 6FF8 GTP 50
72 6HDU GTP 50
73 6FF8 GTP 50
74 6HDU GTP 50
75 1NF3 GNP 50
76 1NF3 GNP 50
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