Receptor
PDB id Resolution Class Description Source Keywords
1KSH 1.8 Å EC: 3.1.4.17 COMPLEX OF ARL2 AND PDE DELTA, CRYSTAL FORM 2 (NATIVE) MUS MUSCULUS SMALL GTPASE SMALL GTP-BINDING PROTEIN ARF FAMILY EFFECTOR MOLECULE IMMUNOGLOBULINE-LIKE FOLD GDI SIGNALING PROTEIN/HYDROLASE COMPLEX
Ref.: THE COMPLEX OF ARL2-GTP AND PDE DELTA: FROM STRUCTURE TO FUNCTION. EMBO J. V. 21 2095 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:201;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:202;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
PO4 A:203;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KSH 1.8 Å EC: 3.1.4.17 COMPLEX OF ARL2 AND PDE DELTA, CRYSTAL FORM 2 (NATIVE) MUS MUSCULUS SMALL GTPASE SMALL GTP-BINDING PROTEIN ARF FAMILY EFFECTOR MOLECULE IMMUNOGLOBULINE-LIKE FOLD GDI SIGNALING PROTEIN/HYDROLASE COMPLEX
Ref.: THE COMPLEX OF ARL2-GTP AND PDE DELTA: FROM STRUCTURE TO FUNCTION. EMBO J. V. 21 2095 2002
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 1KSG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 1KSH - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1KSG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 1KSH - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1KSG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 1KSH - GDP C10 H15 N5 O11 P2 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 : 1KSH; Ligand: GDP; Similar sites found with APoc: 138
This union binding pocket(no: 1) in the query (biounit: 1ksh.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 3MD0 GDP 5.26316
2 4NCN GTP 6.45161
3 4TMZ GSP 6.45161
4 2QN6 GDP 7.23684
5 4RD0 GDP 7.23684
6 3WY9 GDP 7.52688
7 3WYA GDP 7.52688
8 3Q72 GNP 7.83133
9 2WIC GNP 8.60215
10 5YT0 GDP 9.13978
11 5FG3 GDP 9.13978
12 6G14 G4P 9.13978
13 4LC1 GDP 10.089
14 4U5X GNP 10.1124
15 5M04 GDP 10.2151
16 5H7J GCP 10.2151
17 5H7K GDP 10.2151
18 1SKQ GDP 10.7527
19 4ZKD GDP 11.1842
20 1G7C 5GP 11.828
21 3EC1 GDP 11.8421
22 1WDT GTP 11.8421
23 2C5L GTP 11.9658
24 6D5E GNP 12.5
25 6D5H GNP 12.5
26 6BVJ GNP 12.5
27 6D5J GNP 12.5
28 6BVK GNP 12.5
29 6D5G GNP 12.5
30 5W76 GDP 12.9032
31 4DCT GDP 13.4409
32 2HCJ GDP 13.8158
33 1KK1 GNP 13.9785
34 3CNL GNP 14.5161
35 5CK5 GDP 14.5161
36 2WMO GTP 14.5161
37 5GOE GDP 14.5161
38 1A4R GDP 14.5161
39 4B47 GDP 14.6006
40 2J0V GDP 15.0538
41 1DS6 GDP 16.129
42 1I4D GDP 16.129
43 2W2X GSP 16.2162
44 2FJU GSP 16.8539
45 1E96 GTP 17.2043
46 3VMF GTP 17.7632
47 3U6B GDP 18.2796
48 4P3Y GDP 18.2796
49 1D8T GDP 18.2796
50 5JBQ GDP 18.2796
51 4G5G GDP 18.2796
52 3U6K GDP 18.2796
53 2BVN GNP 18.2796
54 4PC3 GDP 18.2796
55 2XTZ GSP 18.8172
56 4J0Q GDP 19.3548
57 2RCN GDP 19.3548
58 5W75 GDP 19.3548
59 4DKX GDP 19.8925
60 2C78 GNP 19.8925
61 2C77 GNP 19.8925
62 6AU6 GDP 20.9677
63 3GJ3 GDP 21.5054
64 3GJ8 GDP 21.5054
65 3GJ7 GDP 21.5054
66 5BXQ GDP 21.5054
67 3GJ0 GDP 21.5054
68 3CH5 GDP 21.5054
69 3GJ5 GDP 21.5054
70 3GJ4 GDP 21.5054
71 5UWQ GNP 21.5054
72 4HAT GNP 21.5054
73 5UWO GNP 21.5054
74 1VG0 GDP 21.5054
75 1VG8 GNP 21.5054
76 1VG1 GDP 21.6216
77 1VG9 GDP 21.6216
78 1TAD GDP 22.043
79 1TAD ALF 22.043
80 1EK0 GNP 22.3529
81 5LEF GTP 22.7273
82 1YRB GDP 23.1183
83 2EW1 GNP 23.6559
84 5HCN GCP 23.6559
85 1S8F GDP 25.4237
86 5W7Q GDP 25.8065
87 1KMQ GNP 27.7174
88 3Q85 GNP 27.8107
89 2GCO GNP 27.957
90 4D0N GDP 28.1081
91 6BCB GSP 28.1081
92 6BC0 GSP 28.1081
93 6BCA GSP 28.1081
94 5UPK GNP 28.2895
95 2CJW GDP 28.4946
96 4D0G GTP 28.5714
97 1CXZ GSP 28.5714
98 3WYF GTP 29.0323
99 3M1I GTP 29.0323
100 4XSH GSP 29.0503
101 2EFE GNH 29.2818
102 3WYG GTP 29.6703
103 1KY3 GDP 29.6703
104 4HDO GNP 29.9401
105 1GUA GNP 29.9401
106 2WJG GDP 30.6452
107 5WLB GNP 30.7229
108 2HT6 GDP 31.0345
109 4LX0 BEF GDP 31.0734
110 2HV8 GTP 31.3953
111 1Z0A GDP 31.6092
112 5UWS GNP 31.8182
113 3MJH GTP 32.1429
114 2Y8E GNP 32.4022
115 2G77 GDP 33.3333
116 1Z06 GNP 33.3333
117 1TU3 GNP 33.3333
118 1WA5 GTP 33.5227
119 5XC5 GTP 33.5227
120 3RAB GNP 33.7278
121 2FFQ GSP 33.9181
122 1MKY GDP 34.4086
123 3TKL GTP 34.4086
124 3QBT GNP 34.4828
125 1YZQ GNP 34.7059
126 5O74 GDP 35.5556
127 1D5C GDP 35.8025
128 1NRJ GTP 37.6344
129 2BME GNP 38.7097
130 3BC1 GNP 38.8158
131 3T12 GDP ALF 39.2473
132 5UWU GNP 40
133 1Z0K GTP 41.2791
134 2FH5 GTP 42.4731
135 1M2O GNP 43.0108
136 1Z0J GTP 46.4706
137 1YVD GNP 47.3373
138 2QTV GNP 47.9042
139 1F6B GDP 50
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