Receptor
PDB id Resolution Class Description Source Keywords
5E95 1.4 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF MB(NS1)/H-RAS COMPLEX HOMO SAPIENS H-RAS MONOBODY INHIBITOR COMPLEX SIGNALING PROTEIN-INHIBCOMPLEX
Ref.: INHIBITION OF RAS FUNCTION THROUGH TARGETING AN ALL REGULATORY SITE. NAT. CHEM. BIOL. V. 13 62 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:201;
Valid;
none;
Kd = 15.7 nM
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:202;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5E95 1.4 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF MB(NS1)/H-RAS COMPLEX HOMO SAPIENS H-RAS MONOBODY INHIBITOR COMPLEX SIGNALING PROTEIN-INHIBCOMPLEX
Ref.: INHIBITION OF RAS FUNCTION THROUGH TARGETING AN ALL REGULATORY SITE. NAT. CHEM. BIOL. V. 13 62 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1579 families.
1 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 6OB3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
4 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
5 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
3 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
4 6H46 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
10 6OB3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
12 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
13 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
14 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
15 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
16 3TNF - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
17 1ZC4 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
18 2A9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
19 2A78 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 3TKL - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
22 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
23 3SFV - 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 : 5E95; Ligand: GDP; Similar sites found with APoc: 68
This union binding pocket(no: 1) in the query (biounit: 5e95.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 6A8D GDP None
2 5M04 GDP 4.16667
3 5KUT GDP 6.34921
4 5KUT GDP 6.34921
5 5KUT GDP 6.34921
6 2HCJ GDP 6.54762
7 1D8T GDP 6.54762
8 1D8T GDP 6.54762
9 1D2E GDP 8.92857
10 1D2E GDP 8.92857
11 2RCN GDP 9.27835
12 2RCN GDP 9.27835
13 5HCN GCP 9.27835
14 4LC1 GDP 9.27835
15 4LC1 GDP 9.27835
16 1KK1 GNP 9.52381
17 2WJG GDP 11.9048
18 4NON GDP 12.5
19 3TK1 GDP 13.4021
20 3TK1 GDP 13.4021
21 3PQC GDP 14.2857
22 3MD0 GDP 14.433
23 1MKY GDP 15.4762
24 2AWN ADP 16.0714
25 2AWN ADP 16.0714
26 2AWN ADP 16.0714
27 5CK5 GDP 18.4524
28 5CK5 GDP 18.4524
29 5CK5 GDP 18.4524
30 5CK5 GDP 18.4524
31 3EC1 GDP 21.6495
32 3EC1 GDP 21.6495
33 4B47 GDP 27.9762
34 1YRB GDP 29.1667
35 1YRB GDP 29.1667
36 5YT0 GDP 31.5476
37 5FG3 GDP 31.5476
38 1S9D GDP 32.1429
39 4DCT GDP 32.1429
40 1RE0 GDP 32.1429
41 4DCT GDP 32.1429
42 2QN6 GDP 33.3333
43 1YZG GDP 33.3333
44 1ZJ6 G3D 33.9286
45 1ZJ6 G3D 33.9286
46 1ZJ6 G3D 33.9286
47 1FZQ GDP 39.881
48 1MR3 G3D 43.4524
49 1SVI GDP 44.6429
50 3A1S GDP 44.6429
51 3A1S GDP 44.6429
52 3GJ4 GDP 48.2143
53 3GJ5 GDP 48.2143
54 3GJ7 GDP 48.2143
55 3GJ8 GDP 48.2143
56 3GJ5 GDP 48.2143
57 3GJ4 GDP 48.2143
58 3GJ7 GDP 48.2143
59 3GJ8 GDP 48.2143
60 1D5C GDP 48.7654
61 5BXQ GDP 48.8095
62 3GJ0 GDP 48.8095
63 5BXQ GDP 48.8095
64 3GJ3 GDP 48.8095
65 5BXQ GDP 48.8095
66 3CH5 GDP 48.8095
67 3CH5 GDP 48.8095
68 3GJ0 GDP 48.8095
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