Receptor
PDB id Resolution Class Description Source Keywords
5SZH 2.3 Å NON-ENZYME: OTHER STRUCTURE OF HUMAN RAB1B IN COMPLEX WITH THE BMERB DOMAIN OF HOMO SAPIENS MICAL-CL DUF3585 MICAL RAB EFFECTOR RAB1B PROTEIN TRANSENDOCYTOSIS
Ref.: BMERB DOMAINS ARE BIVALENT RAB8 FAMILY EFFECTORS EV GENE DUPLICATION. ELIFE V. 5 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:302;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
GNP B:301;
Valid;
none;
submit data
522.196 C10 H17 N6 O13 P3 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5SZH 2.3 Å NON-ENZYME: OTHER STRUCTURE OF HUMAN RAB1B IN COMPLEX WITH THE BMERB DOMAIN OF HOMO SAPIENS MICAL-CL DUF3585 MICAL RAB EFFECTOR RAB1B PROTEIN TRANSENDOCYTOSIS
Ref.: BMERB DOMAINS ARE BIVALENT RAB8 FAMILY EFFECTORS EV GENE DUPLICATION. ELIFE V. 5 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1579 families.
1 5SZH - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1312 families.
1 5SZH - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1130 families.
1 5SZH - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GNP; Similar ligands found: 137
No: Ligand ECFP6 Tc MDL keys Tc
1 9GM 1 1
2 GNP 1 1
3 GDP 0.839506 0.973684
4 GP3 0.82716 0.948718
5 GTP 0.809524 0.973684
6 GNH 0.807229 0.986842
7 GCP 0.77907 0.948718
8 G1R 0.77907 0.961039
9 GSP 0.770115 0.925
10 5GP 0.756098 0.960526
11 G 0.756098 0.960526
12 G2R 0.747253 0.936709
13 GMV 0.747126 0.948718
14 GAV 0.714286 0.936709
15 GP2 0.712644 0.936709
16 G2P 0.711111 0.936709
17 Y9Z 0.708333 0.880952
18 GDD 0.690722 0.936709
19 GKE 0.690722 0.936709
20 GDC 0.690722 0.936709
21 G5P 0.686869 0.948718
22 GPG 0.684211 0.936709
23 GFB 0.683673 0.936709
24 GDR 0.683673 0.936709
25 GTG 0.683673 0.91358
26 JB2 0.68 0.936709
27 GKD 0.68 0.936709
28 6CK 0.676768 0.91358
29 G3A 0.676768 0.948718
30 GDX 0.673267 0.948718
31 ALF 5GP 0.67033 0.86747
32 YGP 0.663265 0.879518
33 GPD 0.656863 0.902439
34 GDP AF3 0.645833 0.86747
35 GDP ALF 0.645833 0.86747
36 ALF GDP 0.645833 0.86747
37 JB3 0.641509 0.925
38 DBG 0.640351 0.974359
39 G3D 0.638298 0.960526
40 G4P 0.625 0.960526
41 GMP 0.621951 0.857143
42 NGD 0.62037 0.936709
43 GGM 0.618182 0.925926
44 0O2 0.616162 0.960526
45 KB7 0.612903 0.807229
46 2MD 0.603604 0.870588
47 CAG 0.60177 0.904762
48 FEG 0.590909 0.858824
49 U2G 0.590909 0.91358
50 GDP 7MG 0.590476 0.888889
51 MGD 0.587719 0.870588
52 G G 0.586538 0.924051
53 ZGP 0.585586 0.848837
54 CG2 0.580357 0.91358
55 KBD 0.568627 0.807229
56 ANP 0.568421 0.922078
57 PGD 0.567797 0.902439
58 MD1 0.567797 0.870588
59 3GP 0.56044 0.922078
60 TPG 0.558333 0.822222
61 GH3 0.55 0.948052
62 KBJ 0.54717 0.77907
63 FE9 0.546219 0.778947
64 GPX 0.539216 0.922078
65 G4M 0.539062 0.860465
66 DGI 0.536082 0.9
67 BGO 0.535088 0.901235
68 IDP 0.53125 0.947368
69 DGT 0.53 0.9
70 2GP 0.526882 0.935065
71 G1R G1R 0.520325 0.901235
72 GCP G 0.518868 0.897436
73 A G 0.516949 0.911392
74 U A G G 0.512605 0.911392
75 AGO 0.504202 0.91358
76 G A A A 0.504202 0.9
77 G1G 0.5 0.902439
78 P2G 0.5 0.860759
79 R7I 0.49505 0.922078
80 R5I 0.49505 0.922078
81 MGP 0.49505 0.936709
82 PGD O 0.492063 0.831461
83 6G0 0.490196 0.936709
84 P1G 0.489796 0.85
85 AKW 0.483051 0.869048
86 DG 0.474227 0.8875
87 DGP 0.474227 0.8875
88 G U 0.466667 0.878049
89 IMP 0.463918 0.934211
90 G2Q 0.462963 0.936709
91 GPC 0.459677 0.858824
92 G C 0.459016 0.878049
93 GTA 0.448276 0.91358
94 G7M 0.444444 0.924051
95 MAP 0.439252 0.898734
96 G G G RPC 0.435484 0.853659
97 ADP 0.434343 0.896104
98 AP5 0.434343 0.871795
99 B4P 0.434343 0.871795
100 A2D 0.43299 0.871795
101 AT4 0.43 0.8625
102 G G G C 0.426357 0.890244
103 AU1 0.425743 0.922078
104 SGP 0.425743 0.807229
105 BA3 0.424242 0.871795
106 C2E 0.423077 0.897436
107 35G 0.423077 0.909091
108 PCG 0.423077 0.909091
109 A G C C 0.423077 0.888889
110 APC G U 0.421875 0.864198
111 HEJ 0.421569 0.896104
112 ATP 0.421569 0.896104
113 5GP 5GP 0.419048 0.860759
114 ACQ 0.419048 0.873418
115 AQP 0.417476 0.896104
116 5FA 0.417476 0.896104
117 01G 0.417391 0.880952
118 AN2 0.415842 0.909091
119 UNP 0.415842 0.810127
120 6AD 0.415094 0.821429
121 M33 0.411765 0.860759
122 ITT 0.411765 0.846154
123 G C C C 0.410448 0.901235
124 JSQ 0.409524 0.851852
125 HFD 0.409524 0.851852
126 G U34 0.408 0.86747
127 ACP 0.407767 0.873418
128 KG4 0.407767 0.873418
129 6YZ 0.407407 0.873418
130 APR 0.403846 0.871795
131 AR6 0.403846 0.871795
132 DG DG 0.403509 0.845238
133 A4P 0.403226 0.848837
134 UCG 0.402985 0.888889
135 AGS 0.4 0.851852
136 SAP 0.4 0.851852
137 AD9 0.4 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5SZH; Ligand: GNP; Similar sites found with APoc: 138
This union binding pocket(no: 1) in the query (biounit: 5szh.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 4LC1 GDP 5.22876
2 4LC1 GDP 5.22876
3 5YT0 GDP 5.91133
4 2AWN ADP 6.40394
5 2AWN ADP 6.40394
6 2AWN ADP 6.40394
7 2AWN ADP 6.40394
8 4DCT GDP 6.89655
9 4DCT GDP 6.89655
10 5FG3 GDP 7.18954
11 2BVN GNP 7.38916
12 1D8T GDP 7.38916
13 1GOJ ADP 8.86699
14 6G14 G4P 9.15033
15 1YRB GDP 9.35961
16 1YRB GDP 9.35961
17 2XTZ GSP 9.80392
18 2XTZ GSP 9.80392
19 3EC1 GDP 9.85222
20 5CK5 GDP 11.1111
21 5CK5 GDP 11.1111
22 5CK5 GDP 11.1111
23 2C77 GNP 11.1111
24 2VVG ADP 13.3005
25 2VVG ADP 13.3005
26 1FQK ALF 14.966
27 2WJG GDP 16.9935
28 4NCN GTP 18.2266
29 4NCN GTP 18.2266
30 1SKQ GDP 18.9542
31 6IZW GSP 23.6453
32 1FQJ ALF 23.8095
33 4RD0 GDP 25.1232
34 3PQC GDP 25.1282
35 1NRJ GTP 26.6055
36 1F6B GDP 26.7677
37 1F6B GDP 26.7677
38 4BAS GNP 27.1357
39 4M9Q GNP 29.5567
40 4M9Q GNP 29.5567
41 4M9Q GNP 29.5567
42 6A8D GDP 30.7292
43 1ZD9 GDP 30.8511
44 1KK1 GNP 31.5271
45 2WKQ GTP 32.0197
46 5KUT GDP 32.2751
47 5KUT GDP 32.2751
48 1ZJ6 G3D 33.1551
49 1DS6 GDP 33.3333
50 1E96 GTP 33.3333
51 1I4D GDP 33.8542
52 2W2X GSP 34.5946
53 2W2X GSP 34.5946
54 1MH1 GNP 34.9462
55 3SBD GNP 35.2941
56 3SBD GNP 35.2941
57 2QN6 GDP 35.4839
58 1FZQ GDP 35.9116
59 2A5F GTP 36
60 2FJU GSP 36.5169
61 2FH5 GTP 38.9163
62 2FH5 GTP 38.9163
63 2FH5 GTP 38.9163
64 1GWN GTP 40.3941
65 1GWN GTP 40.3941
66 1O3Y GTP 41.5663
67 3REF GDP 41.7526
68 1M7B GTP 41.8478
69 5XC5 GTP 42.0455
70 1RE0 GDP 42.0732
71 1NF3 GNP 42.5641
72 1NF3 GNP 42.5641
73 1NF3 GNP 42.5641
74 1NF3 GNP 42.5641
75 2GCO GNP 42.7861
76 2GCN GDP 42.7861
77 3GJ5 GDP 43.3498
78 3GJ4 GDP 43.3498
79 3GJ7 GDP 43.3498
80 3GJ5 GDP 43.3498
81 5UWQ GNP 43.8424
82 5DIF GNP 43.8424
83 5UWW GNP 43.8424
84 5UWP GNP 43.8424
85 5UWJ GNP 43.8424
86 5UWO GNP 43.8424
87 5UWR GNP 43.8424
88 5UWI GNP 43.8424
89 6CIT GNP 43.8424
90 5UWT GNP 43.8424
91 5UWU GNP 43.8424
92 5UWS GNP 43.8424
93 5UWH GNP 43.8424
94 5DHF GNP 43.8424
95 3M1I GTP 43.8424
96 5DI9 GNP 43.8424
97 1UPT GTP 43.8596
98 1UPT GTP 43.8596
99 1UPT GTP 43.8596
100 1UPT GTP 43.8596
101 1A4R GNH 43.9791
102 1A4R GDP 43.9791
103 1GRN GDP 43.9791
104 1GRN AF3 43.9791
105 2J0V GDP 44.335
106 2J0V GDP 44.335
107 5UPK GNP 44.8649
108 5IRC GDP 45.1613
109 5IRC GDP 45.1613
110 1KMQ GNP 45.6522
111 1R4A GNP 46.0606
112 1R4A GNP 46.0606
113 1R4A GNP 46.0606
114 3Q85 GNP 46.1538
115 5HPY GDP 47.027
116 6BSX GDP 47.191
117 6BSX E7S 47.191
118 6BSX GDP 47.191
119 1CXZ GSP 47.2527
120 4HAT GNP 47.7833
121 5BXQ GDP 47.7833
122 5BXQ GDP 47.7833
123 1IBR GNP 47.7833
124 1IBR GNP 47.7833
125 3GJ0 GDP 47.7833
126 3GJ3 GDP 47.7833
127 5BXQ GDP 47.7833
128 3CH5 GDP 47.7833
129 1TX4 ALF GDP 48.0226
130 3Q72 GNP 48.1928
131 4U5X GNP 48.3146
132 1OW3 GDP 48.7047
133 6R3V GDP 49.2228
134 1VG8 GNP 49.7537
135 1VG8 GNP 49.7537
136 1VG8 GNP 49.7537
137 1VG8 GNP 49.7537
138 1VG0 GDP 49.7537
139 2HT6 GDP 50
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