Receptor
PDB id Resolution Class Description Source Keywords
3N5C 1.82 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ARF6DELTA13 COMPLEXED WITH GDP HOMO SAPIENS SMALL G PROTEIN ; SMALL GTP-BINDING PROTEIN ARF ADP-RIBOSYFACTOR 6 TRAFFIC ENDOCYTOSIS UNFOLDED PROTEIN PROTEIN T
Ref.: SAXS AND X-RAY CRYSTALLOGRAPHY SUGGEST AN UNFOLDING FOR THE GDP/GTP CONFORMATIONAL SWITCH OF THE SMALL ARF6. J.MOL.BIOL. V. 402 696 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:1;
A:180;
B:2;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
GDP A:200;
B:200;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3N5C 1.82 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ARF6DELTA13 COMPLEXED WITH GDP HOMO SAPIENS SMALL G PROTEIN ; SMALL GTP-BINDING PROTEIN ARF ADP-RIBOSYFACTOR 6 TRAFFIC ENDOCYTOSIS UNFOLDED PROTEIN PROTEIN T
Ref.: SAXS AND X-RAY CRYSTALLOGRAPHY SUGGEST AN UNFOLDING FOR THE GDP/GTP CONFORMATIONAL SWITCH OF THE SMALL ARF6. J.MOL.BIOL. V. 402 696 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 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 1O3Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
5 1YZG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 3AQ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 4YLG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 1MR3 - G3D C10 H16 N5 O14 P3 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 : 3N5C; Ligand: GDP; Similar sites found with APoc: 155
This union binding pocket(no: 1) in the query (biounit: 3n5c.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2GJ8 ALF GDP None
2 1CLU DBG None
3 1D2E GDP 1.23457
4 5XKT GNP 1.23457
5 6D5E GNP 2.46914
6 6BVJ GNP 2.46914
7 6D5J GNP 2.46914
8 6BVL GNP 2.46914
9 6D59 GNP 2.46914
10 6BVI GNP 2.46914
11 6D56 GNP 2.46914
12 6D55 GNP 2.46914
13 6D5H GNP 2.46914
14 6D5L GNP 2.46914
15 6BVK GNP 2.46914
16 6D5G GNP 2.46914
17 6BVM GNP 2.46914
18 6D5V GNP 2.46914
19 2C5L GTP 2.5641
20 1KK1 GNP 3.08642
21 2C78 GNP 3.08642
22 2C77 GNP 3.08642
23 1TQ4 GDP 3.08642
24 4RD0 GDP 4.32099
25 2QN6 GDP 4.32099
26 2RCN GDP 4.32099
27 2BVN GNP 4.83461
28 1D8T GDP 4.83461
29 1SKQ GDP 4.93827
30 3EC1 GDP 4.93827
31 2UZI GTP 5.26316
32 2HCJ GDP 5.67164
33 1WQ1 GDP 6.17284
34 4LC1 GDP 6.17284
35 1YRB GDP 6.79012
36 2WIC GNP 6.79012
37 3WXM GTP 6.79012
38 4NON GDP 7.40741
39 4B47 GDP 8.02469
40 4R98 GNH 8.02469
41 5FG3 GDP 8.64198
42 5YT0 GDP 8.64198
43 1DAR GDP 8.64198
44 3KUD GDP 8.64198
45 4HI0 GDP 8.64198
46 1LFD GNP 9.1954
47 1WF3 GNP 9.25926
48 3DDC GNP 9.25926
49 1G7S GDP 9.87654
50 5M04 GDP 11.1111
51 3MD0 GDP 11.7284
52 3TK1 GDP 11.7284
53 1MKY GDP 12.3457
54 1X1R GDP 12.963
55 6G14 G4P 16.0494
56 1PUJ GNP 17.284
57 3Q85 GNP 17.284
58 5TAR GDP 17.9012
59 5O2T GSP 17.9012
60 5WLB GNP 17.9012
61 6AU6 GDP 24.0741
62 1CS4 GSP 24.0741
63 2XTZ GSP 24.0741
64 2ZEJ GDP 24.0741
65 3CH5 GDP 24.6914
66 4HAT GNP 24.6914
67 5UWP GNP 24.6914
68 5DIF GNP 24.6914
69 5UWQ GNP 24.6914
70 5UWI GNP 24.6914
71 5UWU GNP 24.6914
72 3GJ3 GDP 24.6914
73 6CIT GNP 24.6914
74 3M1I GTP 24.6914
75 5UWR GNP 24.6914
76 5UWW GNP 24.6914
77 5UWH GNP 24.6914
78 5UWS GNP 24.6914
79 5DHF GNP 24.6914
80 5UWJ GNP 24.6914
81 5UWO GNP 24.6914
82 5UWT GNP 24.6914
83 3GJ0 GDP 24.6914
84 5BXQ GDP 24.6914
85 3GJ8 GDP 25.3086
86 3GJ7 GDP 25.3086
87 3GJ4 GDP 25.3086
88 3GJ5 GDP 25.3086
89 1NRJ GTP 26.6055
90 1TAD GDP 27.1605
91 1TAD ALF 27.1605
92 3Q72 GNP 27.1605
93 1GOT GDP 27.7778
94 1GUA GNP 29.0123
95 4HDO GNP 29.0123
96 1FQK GDP 29.6296
97 3T5G GDP 29.6296
98 4DCT GDP 29.6296
99 6CRK GDP 30.2469
100 2OM2 GDP 30.2469
101 1Y3A GDP 30.2469
102 1BH2 GSP 30.2469
103 5KDO GDP 30.2469
104 1GP2 GDP 30.2469
105 1U8Z GDP 30.2469
106 5OCG GNP 30.2469
107 2ODE ALF GDP 30.8642
108 2WJG GDP 31.4815
109 2WJH GDP 31.4815
110 5Z2M GTP 32.0988
111 1Z0F GDP 32.716
112 2D7C GTP 32.716
113 3RWO GDP 32.716
114 1VG9 GDP 32.716
115 1VG1 GDP 32.716
116 1VG0 GDP 32.716
117 3T12 GDP ALF 33.3333
118 3T1O GDP 33.3333
119 2HV8 GTP 33.3333
120 1OIX GDP 33.3333
121 2A5J GDP 33.3333
122 1Z0K GTP 33.3333
123 2FFQ GSP 33.9506
124 4C4P GNP 33.9506
125 1WA5 GTP 33.9506
126 2BME GNP 33.9506
127 2F9L GDP 33.9506
128 1OIV GDP 33.9506
129 2HT6 GDP 34.5679
130 2CJW GDP 34.5679
131 1Z2A GDP 34.5679
132 5CK5 GDP 34.5679
133 1Z08 GNP 35.1852
134 3CX8 GSP 35.8025
135 3AB3 GDP 35.8025
136 1EK0 GNP 35.8025
137 3MJH GTP 36.4198
138 1ZC3 GNP 36.4198
139 3BC1 GNP 37.037
140 2A9K GDP 37.037
141 1Z0J GTP 37.037
142 1YVD GNP 37.6543
143 1KY3 GDP 37.6543
144 1YZN GNP 38.2716
145 3RAB GNP 38.8889
146 5O74 GDP 38.8889
147 3QBT GNP 39.5062
148 2G77 GDP 40.7407
149 1Z06 GNP 40.7407
150 5XC5 GTP 40.7407
151 1D5C GDP 42.5926
152 1Z0A GDP 42.5926
153 2QTV GNP 47.5309
154 1M2O GNP 47.5309
155 1F6B GDP 49.3827
Pocket No.: 2; Query (leader) PDB : 3N5C; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3n5c.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback