Receptor
PDB id Resolution Class Description Source Keywords
4Y0V 1.8 Å NON-ENZYME: OTHER STRUCTURE OF AN ADP RIBOSYLATION FACTOR FROM ENTAMOEBA HISTO 1:IMSS BOUND TO MG-GDP ENTAMOEBA HISTOLYTICA SIGNALING PROTEIN STRUCTURAL GENOMICS SEATTLE STRUCTURAL GCENTER FOR INFECTIOUS DISEASE SSGCID
Ref.: STRUCTURE OF AN ADP-RIBOSYLATION FACTOR, ARF1, FROM ENTAMOEBA HISTOLYTICA BOUND TO MG(2+)-GDP. ACTA CRYSTALLOGR.,SECT.F V. 71 594 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:201;
B:201;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:202;
B:202;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YLG 1.8 Å NON-ENZYME: OTHER STRUCTURE OF AN ADP RIBOSYLATION FACTOR FROM ENTAMOEBA HISTO 1:IMSS BOUND TO MG-GDP ENTAMOEBA HISTOLYTICA HM-1:IMSS SIGNALING PROTEIN STRUCTURAL GENOMICS SEATTLE STRUCTURAL GCENTER FOR INFECTIOUS DISEASE SSGCID
Ref.: STRUCTURE OF AN ADP-RIBOSYLATION FACTOR, ARF1, FROM ENTAMOEBA HISTOLYTICA BOUND TO MG(2+)-GDP. ACTA CRYSTALLOGR.,SECT.F V. 71 594 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1579 families.
1 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4YLG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1312 families.
1 2X77 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 1RRG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1HUR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1YZG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 3AQ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 1MR3 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 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 6A8D - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 1ZD9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 2AL7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 3AQ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 4YLG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
19 1MR3 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
20 4BAS - GNP C10 H17 N6 O13 P3 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 : 4YLG; Ligand: GDP; Similar sites found with APoc: 113
This union binding pocket(no: 1) in the query (biounit: 4ylg.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 3Q72 GNP None
2 3MD0 GDP 2.89017
3 4B47 GDP 3.46821
4 4LC1 GDP 4.04624
5 4LC1 GDP 4.04624
6 5YT0 GDP 4.62428
7 5FG3 GDP 4.62428
8 3PQC GDP 4.62428
9 2AWN ADP 5.20231
10 2AWN ADP 5.20231
11 2AWN ADP 5.20231
12 1SKQ GDP 5.78035
13 1SKQ GDP 5.78035
14 2HCJ GDP 6.35838
15 1YRB GDP 6.35838
16 1D8T GDP 6.35838
17 2BVN GNP 6.35838
18 2BVN GNP 6.35838
19 1YRB GDP 6.35838
20 1MKY GDP 6.93642
21 5HCN GCP 7.51445
22 2WIC GNP 8.67052
23 4R98 GNH 8.67052
24 2QN6 GDP 10.9827
25 6G14 G4P 12.1387
26 6G14 G4P 12.1387
27 3EC1 GDP 12.1387
28 1PUJ GNP 12.1387
29 5CK5 GDP 12.7168
30 5CK5 GDP 12.7168
31 5CK5 GDP 12.7168
32 5CK5 GDP 12.7168
33 5M04 GDP 15.0289
34 1KK1 GNP 16.185
35 6JFK GDP 17.341
36 1I4D GDP 19.6532
37 1DS6 GDP 19.6532
38 3W5J GDP 20.2312
39 3Q85 GNP 21.3018
40 3Q85 GNP 21.3018
41 5BXQ GDP 22.5434
42 5BXQ GDP 22.5434
43 3GJ5 GDP 22.5434
44 3GJ0 GDP 22.5434
45 3GJ3 GDP 22.5434
46 3GJ7 GDP 22.5434
47 3GJ4 GDP 22.5434
48 5BXQ GDP 22.5434
49 3CH5 GDP 22.5434
50 3GJ5 GDP 22.5434
51 3GJ4 GDP 22.5434
52 6AU6 GDP 22.5434
53 4NON GDP 24.2775
54 2CJW GDP 24.8555
55 2HT6 GDP 24.8555
56 2CJW GDP 24.8555
57 2HT6 GDP 24.8555
58 1TAD GDP 26.0116
59 1TAD ALF 26.0116
60 1GOT GDP 26.5896
61 4DCT GDP 27.1676
62 6MHE GDP 27.1676
63 2RCN GDP 27.7457
64 6CRK GDP 27.7457
65 1Y3A GDP 27.7457
66 1GP2 GDP 27.7457
67 5KDO GDP 27.7457
68 2OM2 GDP 27.7457
69 1Z0A GDP 28.3237
70 1Z0A GDP 28.3237
71 1Z0A GDP 28.3237
72 1Z0A GDP 28.3237
73 1Z0A GDP 28.3237
74 1Z0A GDP 28.3237
75 1FQJ GDP 28.3237
76 1Z0A GDP 28.3237
77 1Z0A GDP 28.3237
78 1Z0A GDP 28.3237
79 1Z0A GDP 28.3237
80 1Z0A GDP 28.3237
81 3T1O GDP 29.4798
82 3T12 GDP ALF 29.4798
83 5TB5 GDP 30.2703
84 5TAR GDP 30.2703
85 3T5G GDP 31.2139
86 3AB3 GDP 31.2139
87 1VG1 GDP 31.7919
88 1VG9 GDP 31.7919
89 1VG9 GDP 31.7919
90 1VG0 GDP 31.7919
91 1VG8 GNP 31.7919
92 4D0N GDP 32.3699
93 5WHA GDP 33.5294
94 5WHA GDP 33.5294
95 2FFQ GSP 33.9181
96 5O74 GDP 34.6821
97 5O74 GDP 34.6821
98 5O74 GDP 34.6821
99 5O74 GDP 34.6821
100 2WJG GDP 34.6821
101 2WJG GDP 34.6821
102 1TU3 GNP 35.0877
103 1TU3 GNP 35.0877
104 1TU3 GNP 35.0877
105 3MJH GTP 35.119
106 1S8F GDP 40.4624
107 1S8F GDP 40.4624
108 1S8F GDP 40.4624
109 1S8F GDP 40.4624
110 1D5C GDP 41.9753
111 3BC1 GNP 42.7746
112 1F6B GDP 46.2428
113 1F6B GDP 46.2428
Pocket No.: 2; Query (leader) PDB : 4YLG; Ligand: GDP; Similar sites found with APoc: 101
This union binding pocket(no: 2) in the query (biounit: 4ylg.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 3Q72 GNP None
2 3MD0 GDP 2.89017
3 4B47 GDP 3.46821
4 4LC1 GDP 4.04624
5 4LC1 GDP 4.04624
6 5FG3 GDP 4.62428
7 5YT0 GDP 4.62428
8 2AWN ADP 5.20231
9 2AWN ADP 5.20231
10 1SKQ GDP 5.78035
11 1SKQ GDP 5.78035
12 2HCJ GDP 6.35838
13 1D8T GDP 6.35838
14 1YRB GDP 6.35838
15 2BVN GNP 6.35838
16 2BVN GNP 6.35838
17 1MKY GDP 6.93642
18 2WIC GNP 8.67052
19 4R98 GNH 8.67052
20 2WIC GNP 8.67052
21 2C78 GNP 9.82659
22 2GKS ADP 9.82659
23 2QN6 GDP 10.9827
24 6G14 G4P 12.1387
25 6G14 G4P 12.1387
26 1PUJ GNP 12.1387
27 3EC1 GDP 12.1387
28 5CK5 GDP 12.7168
29 5CK5 GDP 12.7168
30 5CK5 GDP 12.7168
31 5CK5 GDP 12.7168
32 5M04 GDP 15.0289
33 1KK1 GNP 16.185
34 6JFK GDP 17.341
35 3W5J GDP 20.2312
36 2XTZ GSP 20.8092
37 3Q85 GNP 21.3018
38 3Q85 GNP 21.3018
39 5BXQ GDP 22.5434
40 5BXQ GDP 22.5434
41 6AU6 GDP 22.5434
42 3GJ5 GDP 22.5434
43 3GJ3 GDP 22.5434
44 3GJ0 GDP 22.5434
45 3GJ7 GDP 22.5434
46 3GJ4 GDP 22.5434
47 5BXQ GDP 22.5434
48 3CH5 GDP 22.5434
49 3GJ5 GDP 22.5434
50 3GJ4 GDP 22.5434
51 4NON GDP 24.2775
52 2HT6 GDP 24.8555
53 2CJW GDP 24.8555
54 2CJW GDP 24.8555
55 2HT6 GDP 24.8555
56 1TAD GDP 26.0116
57 1TAD ALF 26.0116
58 1GOT GDP 26.5896
59 6MHE GDP 27.1676
60 4DCT GDP 27.1676
61 2RCN GDP 27.7457
62 6CRK GDP 27.7457
63 1Y3A GDP 27.7457
64 5KDO GDP 27.7457
65 1GP2 GDP 27.7457
66 2OM2 GDP 27.7457
67 1Y3A GDP 27.7457
68 2OM2 GDP 27.7457
69 1Z0A GDP 28.3237
70 1Z0A GDP 28.3237
71 1Z0A GDP 28.3237
72 1FQJ GDP 28.3237
73 1Z0A GDP 28.3237
74 1Z0A GDP 28.3237
75 1Z0A GDP 28.3237
76 1Z0A GDP 28.3237
77 1Z0A GDP 28.3237
78 3T1O GDP 29.4798
79 3T12 GDP ALF 29.4798
80 3T1O GDP 29.4798
81 5TB5 GDP 30.2703
82 3AB3 GDP 31.2139
83 3T5G GDP 31.2139
84 1VG1 GDP 31.7919
85 1VG9 GDP 31.7919
86 1VG9 GDP 31.7919
87 5WHA GDP 33.5294
88 5WHA GDP 33.5294
89 5O74 GDP 34.6821
90 5O74 GDP 34.6821
91 2WJG GDP 34.6821
92 5O74 GDP 34.6821
93 5O74 GDP 34.6821
94 2WJG GDP 34.6821
95 1TU3 GNP 35.0877
96 1TU3 GNP 35.0877
97 1S8F GDP 40.4624
98 1S8F GDP 40.4624
99 1S8F GDP 40.4624
100 1F6B GDP 46.2428
101 1F6B GDP 46.2428
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