Receptor
PDB id Resolution Class Description Source Keywords
2wmn 2.39 Å NON-ENZYME: OTHER STRUCTURE OF THE COMPLEX BETWEEN DOCK9 AND CDC42-GDP. HOMO SAPIENS CELL CYCLE ALTERNATIVE SPLICING METHYLATION PRENYLATION LIPOPROTEIN COILED COIL GEFS DOCK9 CDC42 MEMBRANE NUCLEOTIDE PHOSPHOPROTEIN NUCLEOTIDE-BINDING GTP-BINDING POLYMORPHISM CELL MEMBRANE GUANINE-NUCLEOTIDE RELEASING FACTOR
Ref.: ACTIVATION OF RHO GTPASES BY DOCK EXCHANGE FACTORS IS MEDIATED BY A NUCLEOTIDE SENSOR. SCIENCE V. 325 1398 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP B:1178;
 Valid;
 none;
 submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2WMO 2.2 Å NON-ENZYME: OTHER STRUCTURE OF THE COMPLEX BETWEEN DOCK9 AND CDC42. HOMO SAPIENS POLYMORPHISM CELL MEMBRANE PHOSPHOPROTEIN NUCLEOTIDE-BINDING ALTERNATIVE SPLICING GUANINE-NUCLEOTIDE RELEASING FACTOR CELL CYCLE METHYLATION LIPOPROTEIN COILED COIL GTP-BINDING GEFS DOCK9 CDC42 MEMBRANE PRENYLATION
Ref.: ACTIVATION OF RHO GTPASES BY DOCK EXCHANGE FACTORS IS MEDIATED BY A NUCLEOTIDE SENSOR. SCIENCE V. 325 1398 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 2WMO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 2WMN - 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 1331 families.
1 2WMO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 2WMN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 1HE1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5M70 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5M6X - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1OW3 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 2WMO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
6 2WMN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 2NGR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 4XSG - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
9 6SIU - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 3LXR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 3LWN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 3LW8 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 6R3V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 4XOI - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
15 6BCA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
16 1E96 Kd = 2.7 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 5IRC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 5HPY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
19 6BC0 - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
20 2GCO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
21 1CXZ - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
22 6UKA - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
23 4YC7 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
24 4D0N - 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 : 2WMO; Ligand: GTP; Similar sites found with APoc: 96
This union binding pocket(no: 1) in the query (biounit: 2wmo.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2FH5 GTP 5.26316
2 4NON GDP 5.26316
3 3MJH GTP 5.95238
4 3WXM GTP 6.84211
5 3WXM GTP 6.84211
6 2AWN ADP 7.34908
7 2C78 GNP 7.36842
8 2HCJ GDP 10
9 2BVN GNP 10
10 2BVN GNP 10
11 4DCT GDP 13.6842
12 6AU6 GDP 14.2105
13 1KSH GDP 14.5161
14 5YT0 GDP 14.7368
15 4B47 GDP 14.7368
16 3PQC GDP 14.8718
17 5FG3 GDP 15.2632
18 2RCN GDP 15.7895
19 1YRB GDP 15.7895
20 2QN6 GDP 16.129
21 4M9Q GNP 18.4211
22 1O3Y GTP 26.506
23 3Q72 GNP 30.1205
24 1M2O GNP 32.1053
25 1M2O GNP 32.1053
26 1M2O GNP 32.1053
27 1OIV GDP 32.6316
28 1OIV GDP 32.6316
29 1R4A GNP 33.3333
30 1R4A GNP 33.3333
31 1R4A GNP 33.3333
32 3M1I GTP 35.2632
33 3GJ5 GDP 35.2632
34 3GJ7 GDP 35.2632
35 3GJ4 GDP 35.2632
36 5UWU GNP 35.7895
37 5UWP GNP 35.7895
38 1VG8 GNP 35.7895
39 1VG8 GNP 35.7895
40 5UWQ GNP 35.7895
41 4HAT GNP 35.7895
42 5UWS GNP 35.7895
43 1IBR GNP 35.7895
44 5BXQ GDP 35.7895
45 5BXQ GDP 35.7895
46 3GJ3 GDP 35.7895
47 3GJ0 GDP 35.7895
48 5BXQ GDP 35.7895
49 2D7C GTP 36.5269
50 2QTV GNP 36.5269
51 1VG9 GDP 36.7568
52 1VG1 GDP 36.7568
53 1VG9 GDP 36.7568
54 6X2U GNP 37.6404
55 6X2Y GNP 37.6404
56 6X2S GNP 37.6404
57 6CIT GNP 38.0952
58 2CJW GDP 39.4737
59 2CJW GDP 39.4737
60 5UWO GNP 40
61 2A5J GDP 40
62 3BC1 GNP 40.5263
63 3BC1 GNP 40.5263
64 2HT6 GDP 42.5287
65 3RWO GDP 42.7027
66 1TU3 GNP 43.2749
67 1TU3 GNP 43.2749
68 1TU3 GNP 43.2749
69 1Z0K GTP 43.6047
70 1Z0K GTP 43.6047
71 1Z0A GDP 43.6782
72 1Z0A GDP 43.6782
73 1Z0A GDP 43.6782
74 1Z0A GDP 43.6782
75 1Z0A GDP 43.6782
76 1Z0A GDP 43.6782
77 3Q85 GNP 43.787
78 3Q85 GNP 43.787
79 2BME GNP 44.086
80 2BME GNP 44.086
81 1ZC3 GNP 45.7143
82 5TB5 GDP 45.9459
83 5O74 GDP 46.6667
84 5O74 GDP 46.6667
85 5O74 GDP 46.6667
86 5WDR GNP 46.7836
87 1YVD GNP 47.929
88 1G16 GDP 48.2353
89 1G16 GDP 48.2353
90 1GUA GNP 48.503
91 4HDO GNP 48.503
92 2C5L GTP 48.5549
93 2C5L GTP 48.5549
94 4K81 GTP 49.1228
95 6ZIO GDP 49.711
96 6ZIO GDP 49.711
97 1U8Z GDP 50
98 1U8Z GDP 50
Pocket No.: 2; Query (leader) PDB : 2WMO; Ligand: GTP; 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: 2wmo.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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