Receptor
PDB id Resolution Class Description Source Keywords
4KAX 1.85 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE GRP1 PH DOMAIN IN COMPLEX WITH ARF6 HOMO SAPIENS PH DOMAIN PHOSPHOINOSITIDES PROTEIN BINDING-SIGNALING PROTCOMPLEX
Ref.: STRUCTURAL BASIS FOR MEMBRANE RECRUITMENT AND ALLOS ACTIVATION OF CYTOHESIN FAMILY ARF GTPASE EXCHANGE PROC.NATL.ACAD.SCI.USA V. 110 14213 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:1102;
A:204;
B:1103;
B:1104;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
CIT A:203;
 Invalid;
 none;
 submit data
192.124 C6 H8 O7 C(C(=...
K A:205;
 Part of Protein;
 none;
 submit data
39.098 K [K+]
MG A:202;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
GTP A:201;
 Valid;
 none;
 submit data
523.18 C10 H16 N5 O14 P3 c1nc2...
4IP B:1101;
 Valid;
 none;
 submit data
500.075 C6 H16 O18 P4 [C@H]...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4KAX 1.85 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE GRP1 PH DOMAIN IN COMPLEX WITH ARF6 HOMO SAPIENS PH DOMAIN PHOSPHOINOSITIDES PROTEIN BINDING-SIGNALING PROTCOMPLEX
Ref.: STRUCTURAL BASIS FOR MEMBRANE RECRUITMENT AND ALLOS ACTIVATION OF CYTOHESIN FAMILY ARF GTPASE EXCHANGE PROC.NATL.ACAD.SCI.USA V. 110 14213 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4KAX - GTP C10 H16 N5 O14 P3 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 214 families.
1 1FHX Kd = 0.027 uM 4IP C6 H16 O18 P4 [C@H]1([C@....
2 4KAX - GTP C10 H16 N5 O14 P3 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 181 families.
1 1FHX Kd = 0.027 uM 4IP C6 H16 O18 P4 [C@H]1([C@....
2 4KAX - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GTP; Similar ligands found: 155
No: Ligand ECFP6 Tc MDL keys Tc
1 GTP 1 1
2 GP3 0.921053 0.973684
3 GDP 0.909091 1
4 GSP 0.853659 0.948718
5 GNH 0.82716 0.986667
6 G1R 0.819277 0.986667
7 GAV 0.811765 0.961039
8 9GM 0.809524 0.973684
9 GNP 0.809524 0.973684
10 GCP 0.797619 0.973684
11 5GP 0.797468 0.986486
12 G 0.797468 0.986486
13 GMV 0.764706 0.973684
14 G2R 0.764045 0.961039
15 G5P 0.755319 0.973684
16 GTG 0.752688 0.936709
17 G2P 0.747126 0.961039
18 G3A 0.744681 0.973684
19 GDD 0.741935 0.961039
20 GDC 0.741935 0.961039
21 GKE 0.741935 0.961039
22 0O2 0.736264 0.986486
23 GP2 0.729412 0.961039
24 6CK 0.726316 0.936709
25 Y9Z 0.723404 0.902439
26 GPG 0.717391 0.961039
27 GFB 0.715789 0.961039
28 GDR 0.715789 0.961039
29 GPD 0.704082 0.925
30 GDP BEF 0.696629 0.935065
31 JB2 0.693878 0.961039
32 GKD 0.693878 0.961039
33 GTP MG 0.688889 0.96
34 GDX 0.686869 0.973684
35 ALF 5GP 0.685393 0.888889
36 GH3 0.681319 0.973333
37 YGP 0.677083 0.901235
38 G3D 0.67033 0.986486
39 GDP AF3 0.659574 0.888889
40 GDP ALF 0.659574 0.888889
41 DGT 0.659341 0.923077
42 GMP 0.658228 0.88
43 G4P 0.655914 0.986486
44 JB3 0.653846 0.948718
45 NGD 0.647619 0.961039
46 QBQ 0.644444 0.986486
47 CAG 0.642202 0.880952
48 2MD 0.62963 0.891566
49 MGP 0.619565 0.961039
50 U2G 0.616822 0.936709
51 6G0 0.612903 0.961039
52 MGD 0.612613 0.891566
53 KB7 0.608696 0.82716
54 TPG 0.608696 0.840909
55 CG2 0.605505 0.936709
56 GDP 7MG 0.601942 0.911392
57 FEG 0.601852 0.879518
58 ZGP 0.59633 0.869048
59 PGD 0.591304 0.925
60 MD1 0.591304 0.891566
61 3GP 0.590909 0.946667
62 GPX 0.581633 0.946667
63 CZF 0.580645 0.933333
64 DGI 0.580645 0.923077
65 IDP 0.576087 0.972973
66 DBG 0.567797 0.948718
67 KBD 0.564356 0.82716
68 2GP 0.555556 0.96
69 FE9 0.555556 0.776596
70 G4M 0.547619 0.880952
71 BGO 0.544643 0.924051
72 KBJ 0.542857 0.797619
73 HEJ 0.537634 0.92
74 ATP 0.537634 0.92
75 G1G 0.533898 0.925
76 AQP 0.531915 0.92
77 5FA 0.531915 0.92
78 JSQ 0.520833 0.873418
79 HFD 0.520833 0.873418
80 R7I 0.520408 0.946667
81 R5I 0.520408 0.946667
82 01G 0.518868 0.902439
83 I2C FE2 CMO CMO 0.516667 0.808989
84 ITT 0.510638 0.868421
85 P2G 0.510638 0.883117
86 AKW 0.504348 0.890244
87 GGM 0.504274 0.901235
88 G1R G1R 0.504065 0.924051
89 DG 0.5 0.910256
90 DGP 0.5 0.910256
91 PGD O 0.5 0.850575
92 MGO 0.5 0.864198
93 P1G 0.5 0.871795
94 GTA 0.495495 0.936709
95 PRT 0.490741 0.959459
96 AP5 0.489362 0.894737
97 IMP 0.489362 0.959459
98 B4P 0.489362 0.894737
99 7DT 0.484536 0.906667
100 GPC 0.479339 0.879518
101 G C 0.478992 0.9
102 BA3 0.478723 0.894737
103 ADP 0.473684 0.92
104 G2Q 0.471698 0.961039
105 6YZ 0.470588 0.896104
106 G7M 0.46875 0.948052
107 C1Z 0.462963 0.986486
108 25L 0.458716 0.907895
109 A2D 0.457447 0.894737
110 RGT 0.45045 0.909091
111 AGS 0.45 0.873418
112 SGP 0.44898 0.82716
113 A4P 0.445378 0.869048
114 ANP 0.441176 0.896104
115 8GT 0.441176 0.875
116 ACQ 0.441176 0.896104
117 APC G U 0.440945 0.886076
118 AT4 0.438776 0.884615
119 6AD 0.436893 0.841463
120 UP5 0.432203 0.873418
121 35G 0.431373 0.933333
122 C2E 0.431373 0.921053
123 PCG 0.431373 0.933333
124 5GP 5GP 0.427184 0.883117
125 TAT 0.427184 0.884615
126 T99 0.427184 0.884615
127 APR 0.425743 0.894737
128 AR6 0.425743 0.894737
129 AN2 0.424242 0.907895
130 7DD 0.424242 0.906667
131 AD9 0.421569 0.896104
132 7D4 0.42 0.835443
133 M33 0.42 0.883117
134 UCG 0.419847 0.911392
135 HDV 0.419048 0.825
136 H6Y 0.419048 0.946667
137 GZ0 0.416667 0.948718
138 ACP 0.415842 0.896104
139 T5A 0.414634 0.802326
140 A3R 0.412844 0.839506
141 MGQ 0.412844 0.935897
142 A1R 0.412844 0.839506
143 ADQ 0.412844 0.871795
144 HQG 0.411215 0.907895
145 MGT 0.411215 0.823529
146 93A 0.41 0.833333
147 A22 0.407407 0.907895
148 CA0 0.405941 0.896104
149 ATF 0.40566 0.884615
150 M7G A2M G 0.405229 0.808989
151 AGO 0.404762 0.888889
152 NYZ 0.403846 0.935897
153 KG4 0.401961 0.896104
154 MGV 0.401786 0.890244
155 CGP 0.4 0.86747
Ligand no: 2; Ligand: 4IP; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 4IP 1 1
2 I3P 0.724138 0.966667
3 I3S 0.724138 0.966667
4 IP5 0.714286 0.965517
5 5IP 0.714286 0.965517
6 5MY 0.714286 0.965517
7 I5P 0.714286 0.965517
8 I4P 0.653846 0.965517
9 I0P 0.62069 0.933333
10 ITP 0.6 0.966667
11 2IP 0.571429 0.966667
12 IHP 0.538462 0.965517
13 I6P 0.538462 0.965517
14 IP2 0.533333 0.966667
15 I4D 0.516129 0.933333
Similar Ligands (3D)
Ligand no: 1; Ligand: GTP; Similar ligands found: 41
No: Ligand Similarity coefficient
1 BEF GDP 0.9967
2 ALF GDP 0.9831
3 BEF ADP 0.9768
4 DTP 0.9699
5 8DG 0.9681
6 3AT 0.9677
7 APC 0.9540
8 GDP MG 0.9519
9 ADP BEF 0.9514
10 ADP ALF 0.9503
11 ADP AF3 0.9408
12 ALF ADP 0.9332
13 HF7 0.9242
14 UTP 0.9210
15 DZ4 0.9149
16 CTP 0.9139
17 AMO 0.9072
18 ADP MG 0.9070
19 DSZ 0.8952
20 2KH 0.8870
21 TTP 0.8866
22 6U4 0.8793
23 54H 0.8791
24 VO4 ADP 0.8791
25 EEM 0.8762
26 ATP MG 0.8751
27 SSA 0.8728
28 5AL 0.8707
29 SAM 0.8703
30 KAA 0.8702
31 2TM 0.8697
32 DCP 0.8670
33 DAT 0.8669
34 ADX 0.8660
35 GSU 0.8654
36 SFG 0.8645
37 8X1 0.8616
38 A5A 0.8614
39 D3T 0.8609
40 G5A 0.8580
41 RSN 0.8567
Ligand no: 2; Ligand: 4IP; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4KAX; Ligand: 4IP; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 4kax.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1FAO 4IP 31.746
Pocket No.: 2; Query (leader) PDB : 4KAX; Ligand: GTP; Similar sites found with APoc: 164
This union binding pocket(no: 2) in the query (biounit: 4kax.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2C5L GTP 2.5641
2 2C5L GTP 2.5641
3 1SKQ GDP 4.34783
4 2GJ8 ALF GDP 4.34783
5 2GJ8 ALF GDP 4.34783
6 4RD0 GDP 5.59006
7 1NVV GNP 5.59006
8 1NVV GNP 5.59006
9 1NVV GNP 5.59006
10 6D5E GNP 5.59006
11 6BVJ GNP 5.59006
12 6D55 GNP 5.59006
13 6BVL GNP 5.59006
14 6BVI GNP 5.59006
15 6V9L GNP 5.59006
16 6D5J GNP 5.59006
17 6CUO GNP 5.59006
18 6V9J GNP 5.59006
19 6D5H GNP 5.59006
20 6V9M GNP 5.59006
21 6D5L GNP 5.59006
22 6D59 GNP 5.59006
23 6D56 GNP 5.59006
24 6CUP GNP 5.59006
25 6BVK GNP 5.59006
26 6V94 GNP 5.59006
27 6V9N GNP 5.59006
28 6BVM GNP 5.59006
29 6V9F GNP 5.59006
30 6D5W GNP 5.59006
31 6D5G GNP 5.59006
32 6D5V GNP 5.59006
33 2FFQ GSP 5.91716
34 1YZQ GNP 5.91716
35 1WF3 GNP 8.87574
36 3DDC GNP 9.20245
37 3DDC GNP 9.20245
38 3WXM GTP 9.93789
39 3WXM GTP 9.93789
40 3WXM GTP 9.93789
41 3WXM GTP 9.93789
42 6UKA GNP 10.6509
43 2UZI GTP 11.4035
44 4K81 GTP 12.4224
45 4K81 GTP 12.4224
46 4K81 GTP 12.4224
47 4NCN GTP 13.6646
48 4NCN GTP 13.6646
49 5O2T GSP 16.568
50 2C77 GNP 20.1183
51 2C78 GNP 20.1183
52 1CS4 GSP 22.4852
53 2XTZ GSP 22.4852
54 2XTZ GSP 22.4852
55 2XTZ GSP 22.4852
56 6AU6 GDP 22.4852
57 5UWQ GNP 23.0769
58 5UWP GNP 23.0769
59 4HAT GNP 23.0769
60 5UWW GNP 23.0769
61 5UWU GNP 23.0769
62 5UWR GNP 23.0769
63 5UWT GNP 23.0769
64 5UWI GNP 23.0769
65 5DIF GNP 23.0769
66 5UWJ GNP 23.0769
67 6CIT GNP 23.0769
68 5UWO GNP 23.0769
69 6X2Y GNP 23.0769
70 5DHF GNP 23.0769
71 5UWS GNP 23.0769
72 6X2U GNP 23.0769
73 5BXQ GDP 23.0769
74 5BXQ GDP 23.0769
75 6X2P GNP 23.0769
76 5BXQ GDP 23.0769
77 1IBR GNP 23.0769
78 6X2S GNP 23.0769
79 3M1I GTP 24.8521
80 2BVN GNP 25.4658
81 2BVN GNP 25.4658
82 1TAD GDP 26.0355
83 1TAD ALF 26.0355
84 1NRJ GTP 26.1468
85 1E96 GTP 26.5625
86 3T12 GDP ALF 26.6272
87 5UWH GNP 27.2727
88 6IZW GSP 27.5862
89 1FQJ ALF 27.8107
90 1FQK GDP 27.8107
91 1GUA GNP 28.1437
92 4HDO GNP 28.1437
93 1BH2 GSP 28.4024
94 1SVK ALF GDP 28.9941
95 6S6D GTP 28.9941
96 6S6D GTP 28.9941
97 5WDR GNP 29.2398
98 5WDR GNP 29.2398
99 2ODE ALF GDP 30.1775
100 3CX8 GSP 30.1775
101 1VG8 GNP 30.1775
102 1VG8 GNP 30.1775
103 1VG8 GNP 30.1775
104 1VG8 GNP 30.1775
105 1CXZ GSP 30.1775
106 1VG1 GDP 30.7692
107 5Z2M GTP 31.3609
108 3SBD GNP 31.3609
109 1S8F GDP 31.3609
110 3SBD GNP 31.3609
111 1S8F GDP 31.3609
112 1S8F GDP 31.3609
113 2GCO GNP 31.3609
114 2BME GNP 31.9527
115 2BME GNP 31.9527
116 2BME GNP 31.9527
117 2BME GNP 31.9527
118 4C4P GNP 31.9527
119 2W2X GSP 31.9527
120 2D7C GTP 32.3353
121 2D7C GTP 32.3353
122 1Z0K GTP 32.5444
123 1Z0K GTP 32.5444
124 2HV8 GTP 32.5444
125 2HV8 GTP 32.5444
126 6SGE GTP 32.5444
127 6SGE GTP 32.5444
128 1OIX GDP 32.5444
129 1MH1 GNP 32.5444
130 6HXU GTP 32.5444
131 2HV8 GTP 32.5444
132 1Z08 GNP 33.7278
133 1Z08 GNP 33.7278
134 1TU3 GNP 34.9112
135 1TU3 GNP 34.9112
136 1TU3 GNP 34.9112
137 1TU3 GNP 34.9112
138 1TU3 GNP 34.9112
139 1YVD GNP 35.503
140 1ZC3 GNP 35.503
141 1ZC3 GNP 35.503
142 3MJH GTP 35.7143
143 3MJH GTP 35.7143
144 1Z0J GTP 36.0947
145 3BC1 GNP 36.0947
146 1YZN GNP 36.0947
147 3BC1 GNP 36.0947
148 5UPK GNP 36.0947
149 3RAB GNP 36.6864
150 3QBT GNP 37.2781
151 3QBT GNP 37.2781
152 3QBT GNP 37.2781
153 3QBT GNP 37.2781
154 2FH5 GTP 37.8698
155 2FH5 GTP 37.8698
156 2FH5 GTP 37.8698
157 5XC5 GTP 40.2367
158 1Z0A GDP 40.2367
159 1Z06 GNP 40.8284
160 1EK0 GNP 41.4201
161 1M2O GNP 47.3373
162 1M2O GNP 47.3373
163 1M2O GNP 47.3373
164 1M2O GNP 47.3373
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