Receptor
PDB id Resolution Class Description Source Keywords
5IN4 1.6 Å EC: 4.2.1.47 CRYSTAL STRUCTURE OF GDP-MANNOSE 4,6 DEHYDRATASE BOUND TO A BASED INHIBITOR HOMO SAPIENS GDP-MANNOSE 4 6 DEHYDRATASE ANTIBODY FUCOSYLATION LYASE-ICOMPLEX
Ref.: FACILE MODULATION OF ANTIBODY FUCOSYLATION WITH SMA MOLECULE FUCOSTATIN INHIBITORS AND COCRYSTAL STRUCT GDP-MANNOSE 4,6-DEHYDRATASE. ACS CHEM.BIOL. V. 11 2734 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP B:403;
D:403;
A:1002;
C:1002;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
6CK A:1003;
B:401;
D:401;
C:1003;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 11 uM
643.313 C16 H22 F3 N5 O15 P2 c1nc2...
NAP C:1001;
A:1001;
D:402;
B:402;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5IN4 1.6 Å EC: 4.2.1.47 CRYSTAL STRUCTURE OF GDP-MANNOSE 4,6 DEHYDRATASE BOUND TO A BASED INHIBITOR HOMO SAPIENS GDP-MANNOSE 4 6 DEHYDRATASE ANTIBODY FUCOSYLATION LYASE-ICOMPLEX
Ref.: FACILE MODULATION OF ANTIBODY FUCOSYLATION WITH SMA MOLECULE FUCOSTATIN INHIBITORS AND COCRYSTAL STRUCT GDP-MANNOSE 4,6-DEHYDRATASE. ACS CHEM.BIOL. V. 11 2734 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5IN4 Kd = 11 uM 6CK C16 H22 F3 N5 O15 P2 c1nc2c(n1[....
2 1T2A - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
3 5IN5 Kd = 35 uM GFB C16 H25 N5 O15 P2 C[C@H]1[C@....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5IN4 Kd = 11 uM 6CK C16 H22 F3 N5 O15 P2 c1nc2c(n1[....
2 1T2A - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
3 5IN5 Kd = 35 uM GFB C16 H25 N5 O15 P2 C[C@H]1[C@....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1N7H - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 5IN4 Kd = 11 uM 6CK C16 H22 F3 N5 O15 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
Ligand no: 2; Ligand: 6CK; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 6CK 1 1
2 GDC 0.795918 0.95
3 GDD 0.795918 0.95
4 GKE 0.795918 0.95
5 GFB 0.787879 0.95
6 GDR 0.787879 0.95
7 GDX 0.757282 0.962025
8 GP3 0.73913 0.9375
9 JB2 0.730769 0.95
10 GKD 0.730769 0.95
11 GTP 0.726316 0.936709
12 G1R 0.71875 0.949367
13 GDP 0.712766 0.936709
14 GSP 0.71134 0.891566
15 GPD 0.707547 0.915663
16 JB3 0.706422 0.938272
17 GNH 0.705263 0.925
18 GCP 0.683673 0.91358
19 GNP 0.676768 0.91358
20 9GM 0.676768 0.91358
21 G2R 0.676471 0.902439
22 5GP 0.659574 0.924051
23 G 0.659574 0.924051
24 GMV 0.656566 0.91358
25 GAV 0.631068 0.902439
26 Y9Z 0.62963 0.850575
27 GP2 0.626263 0.902439
28 GTG 0.623853 0.903614
29 GPG 0.622642 0.925926
30 G3A 0.618182 0.9375
31 G5P 0.612613 0.9375
32 G2P 0.61165 0.902439
33 ALF 5GP 0.607843 0.903614
34 YGP 0.590909 0.870588
35 ALF GDP 0.588785 0.903614
36 GDP AF3 0.588785 0.903614
37 GDP ALF 0.588785 0.903614
38 0O2 0.577982 0.924051
39 G4M 0.571429 0.873563
40 U2G 0.571429 0.903614
41 NGD 0.571429 0.925926
42 GMP 0.55914 0.825
43 2MD 0.557377 0.862069
44 CAG 0.556452 0.852273
45 G4P 0.555556 0.924051
46 G G 0.552632 0.91358
47 G3D 0.551402 0.924051
48 CG2 0.54918 0.903614
49 FEG 0.545455 0.872093
50 MGD 0.544 0.862069
51 ZGP 0.540984 0.840909
52 PGD 0.539062 0.892857
53 TPG 0.530769 0.815217
54 GDP 7MG 0.529915 0.879518
55 MD1 0.527132 0.862069
56 DBG 0.519084 0.914634
57 GH3 0.518182 0.9125
58 3GP 0.509804 0.8875
59 FE9 0.507692 0.755102
60 A G 0.492188 0.901235
61 U A G G 0.488372 0.901235
62 DGT 0.486486 0.86747
63 G1R G1R 0.485075 0.914634
64 GPX 0.482456 0.8875
65 R7I 0.481818 0.911392
66 R5I 0.481818 0.911392
67 2GP 0.480769 0.9
68 G A A A 0.48062 0.890244
69 GCP G 0.478632 0.864198
70 ADQ 0.473684 0.864198
71 IDP 0.472222 0.911392
72 G1G 0.466165 0.892857
73 DGI 0.463636 0.86747
74 PGD O 0.459854 0.824176
75 MGP 0.455357 0.902439
76 6G0 0.451327 0.902439
77 BGO 0.449612 0.914634
78 AKW 0.449612 0.860465
79 G U 0.446154 0.869048
80 GPC 0.440298 0.916667
81 GGM 0.439394 0.892857
82 JBT 0.438202 0.77551
83 P2G 0.431193 0.851852
84 G C 0.428571 0.869048
85 G2Q 0.428571 0.902439
86 IMP 0.425926 0.898734
87 P1G 0.423423 0.841463
88 DG 0.422018 0.855422
89 DGP 0.422018 0.855422
90 G G G RPC 0.41791 0.845238
91 GTA 0.417323 0.903614
92 G G G C 0.410072 0.880952
93 A G C C 0.407143 0.879518
94 APC G U 0.405797 0.855422
95 01G 0.4 0.872093
Ligand no: 3; Ligand: NAP; Similar ligands found: 123
No: Ligand ECFP6 Tc MDL keys Tc
1 NAP 1 1
2 NA0 0.881356 0.986301
3 TAP 0.872881 0.934211
4 NDO 0.840336 0.972603
5 NAD 0.811966 0.986111
6 N01 0.733871 0.958904
7 A3D 0.712 0.972603
8 NBP 0.707692 0.935065
9 NHD 0.68254 0.958904
10 NJP 0.661417 0.972973
11 NFD 0.658915 0.934211
12 NXX 0.619048 0.959459
13 DND 0.619048 0.959459
14 AMP NAD 0.606061 0.958904
15 ZID 0.605839 0.972603
16 NAQ 0.59854 0.922078
17 ATR 0.59292 0.917808
18 NAE 0.591241 0.946667
19 NDE 0.58042 0.986301
20 A22 0.571429 0.958904
21 NAJ 0.567164 0.986111
22 A2R 0.563025 0.932432
23 NDC 0.561644 0.922078
24 NA7 0.552846 0.907895
25 ODP 0.551471 0.935065
26 A2P 0.539823 0.930556
27 8ID 0.537313 0.910256
28 NPW 0.525547 0.8875
29 NZQ 0.521739 0.910256
30 CNA 0.521739 0.959459
31 NDP 0.514493 0.922078
32 PO4 PO4 A A A A PO4 0.503937 0.930556
33 1DG 0.503401 0.922078
34 DG1 0.503401 0.922078
35 TXP 0.5 0.922078
36 NMN AMP PO4 0.492958 0.921053
37 XNP 0.492958 0.875
38 25L 0.492308 0.958904
39 25A 0.492063 0.972222
40 NMN 0.486726 0.888889
41 NGD 0.485714 0.935065
42 9JJ 0.481707 0.8875
43 2AM 0.477876 0.891892
44 ADP 0.458333 0.945205
45 PAP 0.451613 0.931507
46 A2D 0.445378 0.945205
47 AN2 0.442623 0.932432
48 7L1 0.441558 0.777778
49 ADP PO3 0.44 0.944444
50 SAP 0.44 0.896104
51 AGS 0.44 0.896104
52 M33 0.439024 0.906667
53 AR6 AR6 0.438849 0.945205
54 BA3 0.438017 0.945205
55 OAD 0.43609 0.92
56 ADP BMA 0.43609 0.92
57 DQV 0.435714 0.958904
58 HEJ 0.435484 0.945205
59 ATP 0.435484 0.945205
60 OOB 0.435115 0.958904
61 B4P 0.434426 0.945205
62 AP5 0.434426 0.945205
63 GAP 0.433071 0.92
64 0WD 0.432432 0.922078
65 2A5 0.432 0.87013
66 5FA 0.432 0.945205
67 AQP 0.432 0.945205
68 AT4 0.430894 0.907895
69 00A 0.428571 0.909091
70 DAL AMP 0.427481 0.932432
71 CA0 0.427419 0.92
72 ADP ALF 0.426357 0.871795
73 ALF ADP 0.426357 0.871795
74 9X8 0.425373 0.871795
75 ACP 0.424 0.92
76 NAJ PZO 0.423841 0.897436
77 9SN 0.423358 0.897436
78 ADP VO4 0.423077 0.932432
79 VO4 ADP 0.423077 0.932432
80 WAQ 0.422222 0.884615
81 V3L 0.421875 0.945205
82 ACQ 0.421875 0.92
83 ADQ 0.421053 0.92
84 AR6 0.420635 0.918919
85 APR 0.420635 0.918919
86 ATP A A A 0.42029 0.958333
87 CO7 0.419753 0.786517
88 3OD 0.419118 0.92
89 1ZZ 0.419118 0.841463
90 DLL 0.41791 0.958904
91 AD9 0.417323 0.92
92 NAX 0.416667 0.875
93 OVE 0.416667 0.857143
94 MYR AMP 0.416058 0.841463
95 AV2 0.415385 0.868421
96 A3P 0.414634 0.944444
97 NNR 0.414414 0.72973
98 OMR 0.413793 0.831325
99 6YZ 0.412214 0.92
100 ANP 0.410853 0.92
101 A1R 0.410448 0.860759
102 ABM 0.409836 0.893333
103 A 0.408333 0.944444
104 AMP 0.408333 0.944444
105 SON 0.408 0.933333
106 PPS 0.407692 0.829268
107 5AL 0.407692 0.932432
108 NAI 0.406897 0.909091
109 7D3 0.406504 0.857143
110 ADX 0.404762 0.829268
111 ATF 0.40458 0.907895
112 3UK 0.404412 0.945946
113 TYR AMP 0.404255 0.921053
114 AMP DBH 0.404255 0.894737
115 139 0.402685 0.875
116 50T 0.401575 0.906667
117 SRP 0.401515 0.907895
118 A A 0.40146 0.972222
119 B5V 0.40146 0.933333
120 A3R 0.4 0.860759
121 3AM 0.4 0.90411
122 B5M 0.4 0.921053
123 FA5 0.4 0.933333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IN4; Ligand: 6CK; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 5in4.bio1) has 135 residues
No: Leader PDB Ligand Sequence Similarity
1 5MSO NAP 4.3956
2 4U7W NDP 4.94506
Pocket No.: 2; Query (leader) PDB : 5IN4; Ligand: 6CK; 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: 5in4.bio1) has 135 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5IN4; Ligand: 6CK; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5in4.bio1) has 134 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5IN4; Ligand: GDP; Similar sites found with APoc: 3
This union binding pocket(no: 4) in the query (biounit: 5in4.bio1) has 133 residues
No: Leader PDB Ligand Sequence Similarity
1 5MSO NAP 4.3956
2 4U7W NDP 4.94506
3 1WVG APR 38.9972
Pocket No.: 5; Query (leader) PDB : 5IN4; Ligand: NAP; Similar sites found with APoc: 2
This union binding pocket(no: 5) in the query (biounit: 5in4.bio1) has 133 residues
No: Leader PDB Ligand Sequence Similarity
1 5MSO NAP 4.3956
2 4U7W NDP 4.94506
Pocket No.: 6; Query (leader) PDB : 5IN4; Ligand: NAP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5in4.bio1) has 133 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5IN4; Ligand: 6CK; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5in4.bio1) has 133 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5IN4; 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: 8) in the query (biounit: 5in4.bio1) has 133 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5IN4; 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: 9) in the query (biounit: 5in4.bio1) has 133 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 5IN4; Ligand: NAP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 5in4.bio1) has 135 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 5IN4; 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: 11) in the query (biounit: 5in4.bio1) has 131 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 5IN4; Ligand: NAP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 5in4.bio1) has 136 residues
No: Leader PDB Ligand Sequence Similarity
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