Receptor
PDB id Resolution Class Description Source Keywords
1I4D 2.5 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPT HOMO SAPIENS COILED COIL G-PROTEIN COMPLEX SIGNALING PROTEIN
Ref.: THE STRUCTURAL BASIS OF ARFAPTIN-MEDIATED CROSS-TAL RAC AND ARF SIGNALLING PATHWAYS. NATURE V. 411 215 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP D:200;
Valid;
none;
Kd = 3 uM
443.201 C10 H15 N5 O11 P2 c1nc2...
MG D:201;
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
1I4D 2.5 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPT HOMO SAPIENS COILED COIL G-PROTEIN COMPLEX SIGNALING PROTEIN
Ref.: THE STRUCTURAL BASIS OF ARFAPTIN-MEDIATED CROSS-TAL RAC AND ARF SIGNALLING PATHWAYS. NATURE V. 411 215 2001
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 1I4D Kd = 3 uM 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 214 families.
1 1I4D Kd = 3 uM 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 181 families.
1 1I4D Kd = 3 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GDP; Similar ligands found: 160
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 GDC 0.747253 0.961039
18 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GPG 0.741573 0.961039
21 GDP BEF 0.741176 0.935065
22 GTP MG 0.732558 0.96
23 G3D 0.732558 0.986486
24 ALF 5GP 0.729412 0.888889
25 Y9Z 0.728261 0.902439
26 G5P 0.723404 0.973684
27 GFB 0.72043 0.961039
28 GTG 0.72043 0.936709
29 GDR 0.72043 0.961039
30 G4P 0.715909 0.986486
31 6CK 0.712766 0.936709
32 G3A 0.712766 0.973684
33 GDP ALF 0.7 0.888889
34 GDP AF3 0.7 0.888889
35 YGP 0.698925 0.901235
36 GKD 0.697917 0.961039
37 JB2 0.697917 0.961039
38 GDX 0.690722 0.973684
39 GPD 0.690722 0.925
40 GMP 0.684211 0.88
41 0O2 0.666667 0.986486
42 JB3 0.656863 0.948718
43 NGD 0.650485 0.961039
44 GDP 7MG 0.636364 0.911392
45 DGI 0.636364 0.923077
46 U2G 0.634615 0.936709
47 GPX 0.634409 0.946667
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 QBQ 0.576087 0.986486
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 KBJ 0.558824 0.797619
69 MGP 0.553191 0.961039
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 I2C FE2 CMO CMO 0.543103 0.808989
73 G1R G1R 0.542373 0.924051
74 P2G 0.527473 0.883117
75 PGD O 0.525 0.850575
76 ADP 0.522222 0.92
77 R5I 0.520833 0.946667
78 R7I 0.520833 0.946667
79 GGM 0.517544 0.901235
80 DG 0.516484 0.910256
81 DGP 0.516484 0.910256
82 P1G 0.516129 0.871795
83 CZF 0.515789 0.933333
84 G1G 0.508475 0.925
85 IMP 0.505495 0.959459
86 AKW 0.504425 0.890244
87 G C 0.504348 0.9
88 GPC 0.491525 0.879518
89 G7M 0.483871 0.948052
90 6AD 0.479592 0.841463
91 ATP 0.473684 0.92
92 HEJ 0.473684 0.92
93 G2Q 0.471154 0.961039
94 AQP 0.46875 0.92
95 5FA 0.46875 0.92
96 GTA 0.468468 0.936709
97 7DD 0.468085 0.906667
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 JSQ 0.459184 0.873418
102 B4P 0.457447 0.894737
103 AP5 0.457447 0.894737
104 A2D 0.456522 0.894737
105 6YZ 0.455446 0.896104
106 ACQ 0.454545 0.896104
107 ANP 0.454545 0.896104
108 5GP 5GP 0.454545 0.883117
109 AT4 0.452632 0.884615
110 APC G U 0.451613 0.886076
111 PRT 0.449541 0.959459
112 ITT 0.447917 0.868421
113 BA3 0.446809 0.894737
114 C2E 0.444444 0.921053
115 35G 0.444444 0.933333
116 PCG 0.444444 0.933333
117 MGO 0.441176 0.864198
118 AN2 0.4375 0.907895
119 NO7 0.436893 0.860759
120 M33 0.43299 0.883117
121 UCG 0.429688 0.911392
122 ACP 0.428571 0.896104
123 MGQ 0.424528 0.935897
124 APR 0.424242 0.894737
125 7DT 0.424242 0.906667
126 AR6 0.424242 0.894737
127 M7G A2M G 0.422819 0.808989
128 93A 0.42268 0.833333
129 A4P 0.420168 0.869048
130 G8D 0.42 0.875
131 AD9 0.42 0.896104
132 AGS 0.42 0.873418
133 CA0 0.418367 0.896104
134 ATF 0.417476 0.884615
135 NYZ 0.415842 0.935897
136 GZ0 0.415254 0.948718
137 AGO 0.414634 0.888889
138 KG4 0.414141 0.896104
139 NIA 0.413043 0.82716
140 MGV 0.412844 0.890244
141 TAT 0.411765 0.884615
142 T99 0.411765 0.884615
143 ADQ 0.411215 0.871795
144 A1R 0.411215 0.839506
145 RGT 0.410714 0.909091
146 CGP 0.409836 0.86747
147 HQG 0.409524 0.907895
148 C1Z 0.409091 0.986486
149 AMP 0.408602 0.893333
150 A 0.408602 0.893333
151 UP5 0.40678 0.873418
152 C2R 0.406593 0.906667
153 AMZ 0.406593 0.918919
154 JBT 0.405882 0.778947
155 A22 0.40566 0.907895
156 25L 0.405405 0.907895
157 ADX 0.40404 0.809524
158 8OD 0.401961 0.946667
159 50T 0.4 0.883117
160 4TC 0.4 0.851852
Similar Ligands (3D)
Ligand no: 1; Ligand: GDP; Similar ligands found: 93
No: Ligand Similarity coefficient
1 ADP MG 0.9864
2 GDP MG 0.9797
3 DAT 0.9680
4 ALF GDP 0.9549
5 A12 0.9524
6 BEF GDP 0.9486
7 AU1 0.9476
8 CUU 0.9442
9 SON 0.9417
10 TYD 0.9414
11 M7G 0.9411
12 ADP ALF 0.9391
13 ADP BEF 0.9391
14 ADP AF3 0.9391
15 BEF ADP 0.9383
16 GAP 0.9328
17 O02 0.9303
18 G5A 0.9285
19 AP2 0.9265
20 5AL 0.9252
21 8GD 0.9250
22 M7M 0.9212
23 AV2 0.9211
24 DAL AMP 0.9209
25 PRX 0.9194
26 UDP 0.9193
27 8LE 0.9188
28 SRP 0.9155
29 SAM 0.9145
30 A5A 0.9126
31 GJV 0.9116
32 NWZ 0.9106
33 CDP 0.9093
34 MGT 0.9090
35 YYY 0.9086
36 5CA 0.9069
37 XMP 0.9066
38 EO7 0.9060
39 SSA 0.9052
40 DSH 0.9051
41 71V 0.9041
42 2A5 0.8973
43 TBD 0.8937
44 CDP MG 0.8931
45 SAH 0.8927
46 IMU 0.8919
47 6RE 0.8917
48 J7C 0.8916
49 7D3 0.8915
50 8LH 0.8914
51 DUD 0.8888
52 NX8 0.8885
53 6CG 0.8882
54 ABM 0.8881
55 8X1 0.8861
56 FMP 0.8855
57 LMS 0.8847
58 8GM 0.8842
59 DTP 0.8842
60 D4D 0.8817
61 C8M 0.8813
62 EEM 0.8812
63 SFG 0.8795
64 8OP 0.8780
65 ADP PO3 0.8775
66 D5M 0.8773
67 IRP 0.8767
68 PAP 0.8765
69 HDV 0.8759
70 ATR 0.8755
71 APC 0.8746
72 N5O 0.8734
73 A3N 0.8728
74 AS 0.8705
75 ATY 0.8684
76 54H 0.8676
77 TSB 0.8674
78 ME8 0.8672
79 HF7 0.8667
80 6MA 0.8654
81 SAI 0.8651
82 DUN 0.8649
83 LSS 0.8640
84 5FU 0.8638
85 P5A 0.8634
86 8QN 0.8633
87 DZ4 0.8609
88 CNU 0.8603
89 NVA LMS 0.8600
90 FNU 0.8593
91 TKW 0.8580
92 MOD 0.8567
93 MSP 0.8549
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1I4D; Ligand: GDP; Similar sites found with APoc: 248
This union binding pocket(no: 1) in the query (biounit: 1i4d.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 2GJ8 ALF GDP 3.48837
2 6J72 GTP 3.64583
3 4M9Q GNP 3.64583
4 4M9Q GNP 3.64583
5 1WF3 GNP 4.6875
6 5W7Q GDP 5.20833
7 5FG3 GDP 5.35714
8 3WYA GDP 5.35714
9 4NON GDP 5.72917
10 4NON GDP 5.72917
11 1SVI GDP 5.72917
12 4RD0 GDP 5.72917
13 3TK1 GDP 6.25
14 3TK1 GDP 6.25
15 2C78 GNP 6.25
16 2QN6 GDP 6.45161
17 5HCN GCP 6.77083
18 4ZKD GDP 7.14286
19 1M2O GNP 7.29167
20 1M2O GNP 7.29167
21 1M2O GNP 7.29167
22 6G14 G4P 7.29167
23 6G14 G4P 7.29167
24 4DCT GDP 7.29167
25 3U6K GDP 8.33333
26 2HCJ GDP 8.33333
27 1D8T GDP 8.33333
28 1D8T GDP 8.33333
29 4G5G GDP 8.33333
30 4B47 GDP 8.33333
31 3U6B GDP 8.33333
32 3U6K GDP 8.33333
33 5JBQ GDP 8.33333
34 3U6B GDP 8.33333
35 4P3Y GDP 8.33333
36 2BVN GNP 8.33333
37 4PC3 GDP 8.33333
38 1YRB GDP 8.85417
39 5W75 GDP 11.4583
40 5W75 GDP 11.4583
41 5W75 GDP 11.4583
42 1TQ4 GDP 12.5
43 2X77 GDP 13.2275
44 2X77 GDP 13.2275
45 3A1S GDP 13.8393
46 3A1S GDP 13.8393
47 4J0Q GDP 15.625
48 4J0Q GDP 15.625
49 4J0Q GDP 15.625
50 4J0Q GDP 15.625
51 4J0Q GDP 15.625
52 3DOE GTP 15.625
53 1KSH GDP 16.129
54 2RCN GDP 16.1458
55 2RCN GDP 16.1458
56 3EC1 GDP 17.7083
57 5EE5 GTP 18.1287
58 4YLG GDP 19.6532
59 1J2J GTP 19.8795
60 4NCN GTP 21.875
61 4TMZ GSP 21.875
62 3PQC GDP 22.3958
63 3PQC GDP 22.3958
64 4ZI2 GNP 24.7368
65 4ZI2 GNP 24.7368
66 4GOJ GNP 24.8677
67 5KUT GDP 25.9259
68 5KUT GDP 25.9259
69 5KUT GDP 25.9259
70 5KSZ GCP 26.5625
71 5KSP GDP 26.8421
72 5YT0 GDP 28.5714
73 1MKY GDP 29.1667
74 6VIK GSP 29.1667
75 1R4A GNP 29.4118
76 1R4A GNP 29.4118
77 1R4A GNP 29.4118
78 1ZD9 GDP 30.3191
79 6ZAY GDP 31.25
80 6ZAY GDP 31.25
81 2G77 GDP 31.25
82 1D2E GDP 31.6964
83 1D2E GDP 31.6964
84 1D2E GDP 31.6964
85 1D2E GDP 31.6964
86 1Z06 GNP 32.2751
87 6IYB GTP 32.8125
88 3WYF GTP 32.8125
89 3WYF GTP 32.8125
90 3E5H GNP 33.1461
91 3E5H GNP 33.1461
92 3GJX GTP 33.3333
93 3GJ5 GDP 33.3333
94 3GJ8 GDP 33.3333
95 3GJ8 GDP 33.3333
96 3GJ7 GDP 33.3333
97 3GJ4 GDP 33.3333
98 3GJ4 GDP 33.3333
99 3GJ7 GDP 33.3333
100 3GJ5 GDP 33.3333
101 1VG0 GDP 33.8542
102 5SZH GNP 33.8542
103 1VG8 GNP 33.8542
104 1VG8 GNP 33.8542
105 1VG8 GNP 33.8542
106 1IBR GNP 33.8542
107 5UWP GNP 33.8542
108 5DIF GNP 33.8542
109 5UWQ GNP 33.8542
110 5UWU GNP 33.8542
111 5UWO GNP 33.8542
112 5UWI GNP 33.8542
113 5UWW GNP 33.8542
114 6CIT GNP 33.8542
115 5UWR GNP 33.8542
116 4HAT GNP 33.8542
117 5UWJ GNP 33.8542
118 6X2U GNP 33.8542
119 6X2Y GNP 33.8542
120 5UWH GNP 33.8542
121 5DHF GNP 33.8542
122 5UWT GNP 33.8542
123 5UWS GNP 33.8542
124 3GJ0 GDP 33.8542
125 3GJ0 GDP 33.8542
126 3GJ3 GDP 33.8542
127 5BXQ GDP 33.8542
128 5BXQ GDP 33.8542
129 5BXQ GDP 33.8542
130 6IF3 GTP 34.4086
131 6IF2 GTP 34.4086
132 3WYG GTP 34.6154
133 1VG9 GDP 35.1351
134 1VG9 GDP 35.1351
135 1VG9 GDP 35.1351
136 1VG9 GDP 35.1351
137 1VG1 GDP 35.1351
138 6X2P GNP 35.2941
139 2EW1 GNP 35.4167
140 3BC1 GNP 35.4167
141 3BC1 GNP 35.4167
142 5O74 GDP 35.5556
143 5O74 GDP 35.5556
144 5O74 GDP 35.5556
145 5O74 GDP 35.5556
146 5O74 GDP 35.5556
147 5Z2M GTP 36.3636
148 5Z2M GTP 36.3636
149 3NKV GNP 36.5714
150 3NKV GNP 36.5714
151 6X2S GNP 37.5
152 3WY9 GDP 37.5
153 3WY9 GDP 37.5
154 5XC5 GTP 38.0682
155 1Z2A GDP 38.0952
156 6HDU GTP 39.1304
157 6HDU GTP 39.1304
158 6HDU GTP 39.1304
159 6HDU GTP 39.1304
160 5OEC GDP 39.3443
161 1Z0J GTP 39.4118
162 6HH2 GDP 40
163 1YVD GNP 40.2367
164 3CPJ GDP 40.625
165 2A5J GDP 40.8377
166 6FF8 GTP 40.884
167 6FF8 GTP 40.884
168 3RWO GDP 41.6216
169 3RWO GDP 41.6216
170 3RWO GDP 41.6216
171 3RWO GDP 41.6216
172 2F9L GDP 42.1875
173 1OIX GDP 42.4084
174 1OIV GDP 42.9319
175 1OIV GDP 42.9319
176 6L6O GDP 43.5028
177 2BME GNP 43.5484
178 2BME GNP 43.5484
179 2BME GNP 43.5484
180 2BME GNP 43.5484
181 3TKL GTP 43.75
182 2EFE GNH 44.1989
183 2EFE GNH 44.1989
184 3Q72 GNP 44.5783
185 3Q72 GNP 44.5783
186 1TU3 GNP 45.614
187 1TU3 GNP 45.614
188 1TU3 GNP 45.614
189 1TU3 GNP 45.614
190 1TU3 GNP 45.614
191 5JCZ GDP 45.8101
192 3MJH GTP 45.8333
193 3MJH GTP 45.8333
194 2CJW GDP 45.8333
195 2CJW GDP 45.8333
196 3SFV GDP 45.8564
197 5UQW GDP 46.0317
198 1Z0K GTP 46.5116
199 1Z0K GTP 46.5116
200 2A9K GDP 46.5241
201 2HT6 GDP 46.5517
202 2HT6 GDP 46.5517
203 6ZSJ GNP 46.6292
204 6ZSJ GNP 46.6292
205 4DKX GDP 46.875
206 4DKX GDP 46.875
207 2Y8E GNP 46.9274
208 2Y8E GNP 46.9274
209 2Y8E GNP 46.9274
210 3T5G GDP 46.9613
211 5TAR GDP 47.027
212 5TB5 GDP 47.027
213 5TB5 GDP 47.027
214 2HV8 GTP 47.093
215 2HV8 GTP 47.093
216 2HV8 GTP 47.093
217 1Z0A GDP 47.1264
218 1Z0A GDP 47.1264
219 1Z0A GDP 47.1264
220 1Z0A GDP 47.1264
221 1Z0A GDP 47.1264
222 1Z0A GDP 47.1264
223 1Z0A GDP 47.1264
224 1Z0A GDP 47.1264
225 1Z0A GDP 47.1264
226 1Z0A GDP 47.1264
227 1Z0A GDP 47.1264
228 1Z0A GDP 47.1264
229 4C4P GNP 47.3988
230 5LEF GTP 47.644
231 5LEF GTP 47.644
232 3QBT GNP 47.7011
233 3QBT GNP 47.7011
234 4LHW GNP 47.7011
235 4LHW GNP 47.7011
236 4LHW GNP 47.7011
237 3QBT GNP 47.7011
238 3QBT GNP 47.7011
239 4LHW GNP 47.7011
240 2D7C GTP 47.9042
241 2D7C GTP 47.9042
242 3Q85 GNP 47.929
243 3Q85 GNP 47.929
244 1D5C GDP 48.1481
245 1Z0F GDP 48.6034
246 1KY3 GDP 48.9011
247 1UAD GNP 49.7143
248 1UAD GNP 49.7143
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