Receptor
PDB id Resolution Class Description Source Keywords
3KUC 1.92 Å EC: 2.7.11.1 COMPLEX OF RAP1A(E30D/K31E)GDP WITH RAFRBD(A85K/N71R) 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
CA B:172;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
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
1GUA 2 Å EC: 2.7.11.1 HUMAN RAP1A, RESIDUES 1-167, DOUBLE MUTANT (E30D,K31E) COMPLEXED WITH GPPNHP AND THE RAS-BINDING-DOMAIN OF HUMAN C -RAF1, RESIDUES 51-131 HOMO SAPIENS ONCOGENE PROTEIN/KINASE/EFFECTOR PROTEIN GTP-BINDING- PROTEIN COMPLEX (GTP-BINDING/ATP-BINDING)
Ref.: RAS/RAP EFFECTOR SPECIFICITY DETERMINED BY CHARGE REVERSAL. NAT.STRUCT.BIOL. V. 3 723 1996
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 117 families.
1 1GUA Kd = 40 nM GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
70% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
2 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
3 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
4 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
10 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
14 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
16 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
17 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
19 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
21 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
22 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
23 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
24 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
25 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
26 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
27 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
28 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
29 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
30 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
31 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
32 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
33 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
34 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
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: GDP; Similar ligands found: 161
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 9GM 0.839506 0.973684
6 GNP 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 GDC 0.747253 0.961039
18 GKE 0.747253 0.961039
19 GDD 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 GFB 0.72043 0.961039
26 GTG 0.72043 0.936709
27 GDR 0.72043 0.961039
28 G4P 0.715909 0.986486
29 G3A 0.712766 0.973684
30 6CK 0.712766 0.936709
31 GDP AF3 0.7 0.888889
32 ALF GDP 0.7 0.888889
33 GDP ALF 0.7 0.888889
34 YGP 0.698925 0.901235
35 GKD 0.697917 0.961039
36 JB2 0.697917 0.961039
37 GDX 0.690722 0.973684
38 GPD 0.690722 0.925
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 DGI 0.636364 0.923077
44 GDP 7MG 0.636364 0.911392
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 CG2 0.622642 0.936709
52 FEG 0.619048 0.879518
53 MGD 0.614679 0.891566
54 ZGP 0.613208 0.869048
55 GH3 0.612903 0.973333
56 3GP 0.611765 0.946667
57 MD1 0.607143 0.891566
58 PGD 0.59292 0.925
59 DGT 0.591398 0.923077
60 BGO 0.588785 0.924051
61 TPG 0.582609 0.840909
62 DBG 0.582609 0.948718
63 2GP 0.574713 0.96
64 FE9 0.570175 0.776596
65 GCP G 0.56 0.921053
66 A G 0.553571 0.935065
67 G A A A 0.553571 0.923077
68 MGP 0.553191 0.961039
69 U A G G 0.548673 0.935065
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 G1R G1R 0.542373 0.924051
73 P2G 0.527473 0.883117
74 PGD O 0.525 0.850575
75 ADP 0.522222 0.92
76 R5I 0.520833 0.946667
77 R7I 0.520833 0.946667
78 GGM 0.517544 0.901235
79 DGP 0.516484 0.910256
80 DG 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G U 0.513274 0.9
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 AKW 0.504425 0.890244
86 G C 0.504348 0.9
87 GPC 0.491525 0.879518
88 G7M 0.483871 0.948052
89 6AD 0.479592 0.841463
90 ATP 0.473684 0.92
91 HEJ 0.473684 0.92
92 G2Q 0.471154 0.961039
93 5FA 0.46875 0.92
94 AQP 0.46875 0.92
95 GTA 0.468468 0.936709
96 7DD 0.468085 0.906667
97 G G G RPC 0.466102 0.875
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 B4P 0.457447 0.894737
102 AP5 0.457447 0.894737
103 A2D 0.456522 0.894737
104 6YZ 0.455446 0.896104
105 G G G C 0.455285 0.9125
106 5GP 5GP 0.454545 0.883117
107 ANP 0.454545 0.896104
108 ACQ 0.454545 0.896104
109 AT4 0.452632 0.884615
110 A G C C 0.451613 0.911392
111 APC G U 0.45082 0.886076
112 PRT 0.449541 0.959459
113 G U34 0.449153 0.888889
114 DG DG 0.448598 0.865854
115 ITT 0.447917 0.868421
116 BA3 0.446809 0.894737
117 C2E 0.444444 0.921053
118 PCG 0.444444 0.933333
119 35G 0.444444 0.933333
120 MGO 0.441176 0.864198
121 AN2 0.4375 0.907895
122 G C C C 0.4375 0.924051
123 M33 0.43299 0.883117
124 UCG 0.429688 0.911392
125 A G U 0.42963 0.888889
126 ACP 0.428571 0.896104
127 MGQ 0.424528 0.935897
128 AR6 0.424242 0.894737
129 7DT 0.424242 0.906667
130 APR 0.424242 0.894737
131 93A 0.42268 0.833333
132 A4P 0.420168 0.869048
133 G8D 0.42 0.875
134 AD9 0.42 0.896104
135 SAP 0.42 0.873418
136 AGS 0.42 0.873418
137 CA0 0.418367 0.896104
138 ATF 0.417476 0.884615
139 AGO 0.414634 0.888889
140 A G U U 0.414286 0.888889
141 NIA 0.413043 0.82716
142 MGV 0.412844 0.890244
143 TAT 0.411765 0.884615
144 T99 0.411765 0.884615
145 ADQ 0.411215 0.871795
146 A1R 0.411215 0.839506
147 RGT 0.410714 0.909091
148 CGP 0.409836 0.86747
149 C1Z 0.409091 0.986486
150 A 0.408602 0.893333
151 AMP 0.408602 0.893333
152 UP5 0.40678 0.873418
153 AMZ 0.406593 0.918919
154 C2R 0.406593 0.906667
155 JBT 0.405882 0.778947
156 A22 0.40566 0.907895
157 25L 0.405405 0.907895
158 ADX 0.40404 0.809524
159 8OD 0.401961 0.946667
160 50T 0.4 0.883117
161 4TC 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1GUA; Ligand: GNP; Similar sites found with APoc: 71
This union binding pocket(no: 1) in the query (biounit: 1gua.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1MR3 G3D None
2 2HCJ GDP 4.79042
3 5HCN GCP 4.93827
4 5W76 GDP 5.38922
5 2C77 GNP 5.98802
6 5KUT GDP 7.18563
7 4LC1 GDP 7.18563
8 4B47 GDP 7.98898
9 1KK1 GNP 8.38323
10 4J0Q GDP 8.64198
11 5M04 GDP 8.64198
12 2RCN GDP 8.98204
13 3WY9 GDP 9.58084
14 3WYA GDP 9.58084
15 2X77 GDP 10.0529
16 1SKQ GDP 10.1796
17 1MKY GDP 11.3772
18 1R4A GNP 11.5152
19 3MD0 GDP 12.3457
20 5CK5 GDP 13.1737
21 1NRJ GTP 13.5802
22 2FH5 GTP 14.3713
23 5W75 GDP 14.3713
24 1UPT GTP 16.0494
25 4NCN GTP 17.9641
26 4TMZ GSP 17.9641
27 5W7Q GDP 17.9641
28 2XTZ GSP 19.1617
29 5EE5 GTP 20.9877
30 4DCT GDP 20.9877
31 3U6B GDP 21.5569
32 4P3Y GDP 21.5569
33 2BVN GNP 21.5569
34 1D8T GDP 21.5569
35 5JBQ GDP 21.5569
36 4G5G GDP 21.5569
37 3U6K GDP 21.5569
38 3CNL GNP 22.2222
39 5FG3 GDP 25.7485
40 4GOJ GNP 26.9461
41 4ZI2 GNP 26.9461
42 1FZQ GDP 26.9461
43 5DI3 GNP 27.5449
44 4KAX GTP 28.1437
45 3N5C GDP 29.0123
46 2W83 GTP 29.0909
47 1YRB GDP 29.9401
48 1KSH GDP 29.9401
49 1YZG GDP 30.5389
50 4M9Q GNP 31.1377
51 1ZJ6 G3D 31.1377
52 5YT0 GDP 31.7365
53 1RE0 GDP 32.0988
54 1J2J GTP 32.0988
55 2J59 GTP 32.0988
56 1O3Y GTP 32.0988
57 3AQ4 GDP 32.0988
58 1ZD9 GDP 35.9281
59 2QN6 GDP 41.9162
60 4RD0 GDP 41.9162
61 3E5H GNP 43.7126
62 1NF3 GNP 47.3054
63 1A4R GNH 47.9042
64 1A4R GDP 47.9042
65 2WMO GTP 48.503
66 1GRN GDP 48.503
67 5OEC GDP 48.503
68 4YC7 GNP 48.503
69 1GRN AF3 48.503
70 1GWN GTP 49.7006
71 1M7B GTP 49.7006
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