Receptor
PDB id Resolution Class Description Source Keywords
1FZQ 1.7 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF MURINE ARL3-GDP MUS MUSCULUS PROTEIN-GDP COMPLEX WITHOUT MAGNESIUM ARF FAMILY RAS SUPERFAMILY G-DOMAIN SIGNALING PROTEIN
Ref.: STRUCTURAL AND BIOCHEMICAL PROPERTIES SHOW ARL3-GDP AS A DISTINCT GTP BINDING PROTEIN. STRUCTURE FOLD.DES. V. 8 1239 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:301;
Valid;
none;
Kd = 24 nM
443.201 C10 H15 N5 O11 P2 c1nc2...
MES A:201;
Invalid;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
NH4 A:501;
Invalid;
none;
submit data
18.038 H4 N [NH4+...
SO4 A:401;
A:402;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1FZQ 1.7 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF MURINE ARL3-GDP MUS MUSCULUS PROTEIN-GDP COMPLEX WITHOUT MAGNESIUM ARF FAMILY RAS SUPERFAMILY G-DOMAIN SIGNALING PROTEIN
Ref.: STRUCTURAL AND BIOCHEMICAL PROPERTIES SHOW ARL3-GDP AS A DISTINCT GTP BINDING PROTEIN. STRUCTURE FOLD.DES. V. 8 1239 2000
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 286 families.
1 1FZQ Kd = 24 nM 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 209 families.
1 1FZQ Kd = 24 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 4V0K - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4V0L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 2X77 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1RRG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 1HUR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 1O3Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 1FZQ Kd = 24 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 1Z6Y - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 1ZJ6 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
10 1YZG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 1ZD9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 2AL7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 3AQ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 4YLG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 1MR3 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
19 4BAS - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
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 : 1FZQ; Ligand: GDP; Similar sites found with APoc: 190
This union binding pocket(no: 1) in the query (biounit: 1fzq.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1SVI GDP 3.31492
2 1YRB GDP 3.8674
3 1KK1 GNP 3.8674
4 5W75 GDP 3.8674
5 5H7J GCP 3.8674
6 2C78 GNP 4.41989
7 5W7Q GDP 4.41989
8 1D2E GDP 4.41989
9 2C77 GNP 4.41989
10 5W76 GDP 4.41989
11 3MD0 GDP 4.41989
12 1DAR GDP 4.41989
13 4RD0 GDP 4.97238
14 3WXM GTP 5.52486
15 1SKQ GDP 5.52486
16 1G7S GDP 6.07735
17 5GOE GDP 6.07735
18 4ZKD GDP 6.62983
19 3U6B GDP 7.18232
20 4P3Y GDP 7.18232
21 2BVN GNP 7.18232
22 5JBQ GDP 7.18232
23 1D8T GDP 7.18232
24 2HCJ GDP 7.18232
25 4G5G GDP 7.18232
26 3EC1 GDP 7.18232
27 3U6K GDP 7.18232
28 4PC3 GDP 7.18232
29 1TQ4 GDP 7.18232
30 4LC1 GDP 7.73481
31 4J0Q GDP 8.28729
32 3WY9 GDP 8.75576
33 3WYA GDP 8.75576
34 5H7K GDP 8.83978
35 2WIC GNP 8.83978
36 1WF3 GNP 9.39227
37 5HCN GCP 11.0497
38 6G14 G4P 12.1547
39 3TK1 GDP 12.7072
40 5FG3 GDP 13.8122
41 3CNL GNP 15.4696
42 2RCN GDP 16.5746
43 2QN6 GDP 17.2043
44 2ZEJ GDP 17.9348
45 1GOT GDP 18.232
46 3VMF GTP 18.7845
47 2XTZ GSP 18.7845
48 1TAD GDP 18.7845
49 1TAD ALF 18.7845
50 2ODE ALF GDP 19.337
51 6CRK GDP 19.337
52 1FQK GDP 19.337
53 2OM2 GDP 19.337
54 1GP2 GDP 19.337
55 5KDO GDP 19.337
56 6AU6 GDP 21.547
57 1CS4 GSP 21.547
58 2WJG GDP 22.6519
59 1Z2A GDP 24.4048
60 2WJH GDP 24.6988
61 3CX8 GSP 24.8619
62 3AB3 GDP 24.8619
63 1ZCB GDP 24.8619
64 3MJH GTP 25.4144
65 1TU3 GNP 25.9669
66 1MKY GDP 26.5193
67 3WYF GTP 26.5193
68 3WYG GTP 26.5193
69 4KVG GTP 26.7857
70 1GUA GNP 26.9461
71 2EFE GNH 27.0718
72 4HDO GNP 27.5449
73 4HDQ GNP 27.5449
74 3Q72 GNP 28.1768
75 2A5J GDP 28.7293
76 4NON GDP 28.7293
77 3GJ8 GDP 29.2818
78 3GJ3 GDP 29.2818
79 3GJ0 GDP 29.2818
80 3GJ7 GDP 29.2818
81 3GJ4 GDP 29.2818
82 3GJ5 GDP 29.2818
83 4HAT GNP 29.2818
84 5UWQ GNP 29.2818
85 5UWP GNP 29.2818
86 6CIT GNP 29.2818
87 5DIF GNP 29.2818
88 1WA5 GTP 29.2818
89 5UWR GNP 29.2818
90 5UWI GNP 29.2818
91 5UWW GNP 29.2818
92 5DHF GNP 29.2818
93 5UWO GNP 29.2818
94 5UWU GNP 29.2818
95 5BXQ GDP 29.2818
96 5UWS GNP 29.2818
97 5UWH GNP 29.2818
98 5UWJ GNP 29.2818
99 2A9K GDP 29.2818
100 1S8F GDP 29.3785
101 5Z2M GTP 29.8343
102 1VG0 GDP 29.8343
103 1Z0J GTP 29.8343
104 3E5H GNP 29.8343
105 1Z0A GDP 29.8343
106 1UAD GNP 30.2857
107 1Z06 GNP 30.3867
108 5YT0 GDP 30.3867
109 3RAB GNP 30.3867
110 3T5G GDP 30.3867
111 1VG9 GDP 30.3867
112 1VG1 GDP 30.3867
113 4DCT GDP 30.3867
114 1YVD GNP 30.3867
115 3CPJ GDP 30.3867
116 1Z08 GNP 30.3867
117 3Q85 GNP 30.7692
118 2CJW GDP 30.9392
119 1OIX GDP 30.9392
120 3RWO GDP 31.4917
121 1OIV GDP 31.4917
122 5OEC GDP 31.4917
123 5JCZ GDP 31.4917
124 5WDR GNP 31.5789
125 2HV8 GTP 31.9767
126 2G77 GDP 32.0442
127 2HT6 GDP 32.1839
128 4C4P GNP 32.3699
129 3BC1 GNP 32.5967
130 2D7C GTP 32.9341
131 1YZN GNP 33.1492
132 1KY3 GDP 33.1492
133 1D5C GDP 33.9506
134 3T12 GDP ALF 34.2541
135 3T1O GDP 34.2541
136 2GJ8 ALF GDP 34.3023
137 2FFQ GSP 34.5029
138 2F9L GDP 34.6734
139 5UWT GNP 34.7826
140 4DKX GDP 35.3591
141 5XC5 GTP 35.3591
142 5SZH GNP 35.9116
143 5LEF GTP 35.9116
144 2EW1 GNP 36.4641
145 5UQW GDP 36.5079
146 1NRJ GTP 37.0166
147 1EK0 GNP 37.0588
148 3NKV GNP 37.1429
149 5TAR GDP 37.2973
150 5TB5 GDP 37.2973
151 1Z0F GDP 37.4302
152 3SFV GDP 37.5691
153 5O74 GDP 37.7778
154 3TKL GTP 38.1215
155 1YZQ GNP 38.2353
156 5OCG GNP 38.674
157 2C5L GTP 38.7283
158 4B47 GDP 39.2265
159 5O2T GSP 39.645
160 1Z0K GTP 39.779
161 5E95 GDP 39.881
162 6BVJ GNP 40.1198
163 6BVL GNP 40.1198
164 6D5J GNP 40.1198
165 6D59 GNP 40.1198
166 6D5L GNP 40.1198
167 6BVI GNP 40.1198
168 6BVK GNP 40.1198
169 6D5E GNP 40.1198
170 6BVM GNP 40.1198
171 6D5H GNP 40.1198
172 6D55 GNP 40.1198
173 6D56 GNP 40.1198
174 6D5G GNP 40.1198
175 6D5V GNP 40.1198
176 5WLB GNP 40.3614
177 3DDC GNP 40.3614
178 2UZI GTP 40.3614
179 1CLU DBG 40.3614
180 3KUD GDP 40.3614
181 1WQ1 GDP 40.3614
182 1LFD GNP 40.7186
183 2BME GNP 40.884
184 5M04 GDP 41.4365
185 3PQC GDP 41.4365
186 3QBT GNP 41.9889
187 4LHW GNP 42.5414
188 1M2O GNP 45.3039
189 1F6B GDP 46.9613
190 2QTV GNP 48.503
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