Receptor
PDB id Resolution Class Description Source Keywords
6CRK 2 Å NON-ENZYME: BINDING HETEROTRIMERIC G-PROTEIN IN COMPLEX WITH AN ANTIBODY FRAGMEN HOMO SAPIENS HETEROTRIMERIC G-PROTEIN ANTIBODY FRAGMENT SIGNALING PROTEI
Ref.: DEVELOPMENT OF AN ANTIBODY FRAGMENT THAT STABILIZES GPCR/G-PROTEIN COMPLEXES. NAT COMMUN V. 9 3712 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:401;
Valid;
none;
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443.201 C10 H15 N5 O11 P2 c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6CRK 2 Å NON-ENZYME: BINDING HETEROTRIMERIC G-PROTEIN IN COMPLEX WITH AN ANTIBODY FRAGMEN HOMO SAPIENS HETEROTRIMERIC G-PROTEIN ANTIBODY FRAGMENT SIGNALING PROTEI
Ref.: DEVELOPMENT OF AN ANTIBODY FRAGMENT THAT STABILIZES GPCR/G-PROTEIN COMPLEXES. NAT COMMUN V. 9 3712 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 544 families.
1 6CRK - GDP C10 H15 N5 O11 P2 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 420 families.
1 6CRK - GDP C10 H15 N5 O11 P2 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 319 families.
1 6CRK - 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 : 6CRK; Ligand: GDP; Similar sites found with APoc: 90
This union binding pocket(no: 1) in the query (biounit: 6crk.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4R98 GNH 4.05904
2 3U6B GDP 5.58376
3 3U6B GDP 5.58376
4 5JBQ GDP 5.58376
5 4G5G GDP 5.58376
6 3U6K GDP 5.58376
7 1D8T GDP 5.59796
8 1D8T GDP 5.59796
9 4P3Y GDP 5.6338
10 5W76 GDP 5.7971
11 5YT0 GDP 5.91549
12 2WIC GNP 5.99251
13 2WIC GNP 5.99251
14 3W5J GDP 6.37255
15 3CNL GNP 6.48855
16 5O74 GDP 6.59898
17 5O74 GDP 6.59898
18 5O74 GDP 6.59898
19 5W7Q GDP 7.04225
20 5FG3 GDP 7.24638
21 1SKQ GDP 7.33591
22 1SKQ GDP 7.33591
23 2AWN ADP 7.82609
24 3MD0 GDP 7.88732
25 1S8F GDP 7.9096
26 1S8F GDP 7.9096
27 1S8F GDP 7.9096
28 1S8F GDP 7.9096
29 5M04 GDP 8.10811
30 2HCJ GDP 8.10811
31 4DKX GDP 8.33333
32 1Z0F GDP 8.37989
33 5H7J GCP 8.4507
34 3TK1 GDP 8.48485
35 3TK1 GDP 8.48485
36 2WJG GDP 8.51064
37 2WJG GDP 8.51064
38 2WJH GDP 9.63855
39 3EC1 GDP 9.7561
40 5GOE GDP 9.85915
41 6HH2 GDP 10.5556
42 4B47 GDP 11.2676
43 3GJ0 GDP 11.3122
44 5BXQ GDP 11.5741
45 5BXQ GDP 11.5741
46 1Z0A GDP 12.069
47 1Z0A GDP 12.069
48 1Z0A GDP 12.069
49 3GJ3 GDP 12.1212
50 4NON GDP 12.6761
51 5H7K GDP 12.6761
52 2RCN GDP 12.6761
53 3Q72 GNP 14.4578
54 2GKS ADP 15.493
55 5CK5 GDP 15.493
56 3GJ5 GDP 17.6471
57 3T1O GDP 17.6768
58 3T1O GDP 17.6768
59 3WYA GDP 18.3099
60 3WY9 GDP 18.3099
61 3WY9 GDP 18.3099
62 3GJ7 GDP 18.3673
63 6G14 G4P 18.7075
64 6G14 G4P 18.7075
65 1FZQ GDP 19.337
66 1ZJ6 G3D 20.3209
67 1ZJ6 G3D 20.3209
68 1F6B GDP 21.7172
69 1F6B GDP 21.7172
70 1YZG GDP 22.3464
71 1MR3 G3D 24.3094
72 3AQ4 GDP 27.1739
73 3AQ4 GDP 27.1739
74 4YLG GDP 27.7457
75 4YLG GDP 27.7457
76 4J0Q GDP 28.169
77 4J0Q GDP 28.169
78 4J0Q GDP 28.169
79 4J0Q GDP 28.169
80 4J0Q GDP 28.169
81 1S9D GDP 29.2683
82 1RE0 GDP 29.2683
83 3N5C GDP 30.2469
84 3N5C GDP 30.2469
85 1KK1 GNP 33.8028
86 5W75 GDP 35.2113
87 5W75 GDP 35.2113
88 5W75 GDP 35.2113
89 5W75 GDP 35.2113
90 2QN6 GDP 44.4444
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