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Receptor
PDB id Resolution Class Description Source Keywords
5KY9 1.83 Å EC: 2.4.1.221 MOUSE POFUT1 IN COMPLEX WITH MOUSE NOTCH1 EGF12 MUTANT (D464 AND GDP MUS MUSCULUS GLYCOSYLTRANSFERASE TRANSFERASE
Ref.: RECOGNITION OF EGF-LIKE DOMAINS BY THE NOTCH-MODIFY O-FUCOSYLTRANSFERASE POFUT1. NAT. CHEM. BIOL. V. 13 757 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:402;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
NAG A:401;
Invalid;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KY9 1.83 Å EC: 2.4.1.221 MOUSE POFUT1 IN COMPLEX WITH MOUSE NOTCH1 EGF12 MUTANT (D464 AND GDP MUS MUSCULUS GLYCOSYLTRANSFERASE TRANSFERASE
Ref.: RECOGNITION OF EGF-LIKE DOMAINS BY THE NOTCH-MODIFY O-FUCOSYLTRANSFERASE POFUT1. NAT. CHEM. BIOL. V. 13 757 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5KY0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5KY8 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5KY9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5KY7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5KY5 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5KY0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 5KY8 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 5KY9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5KY4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5KY7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5KY5 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5KY2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 5KXH - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 5KY3 - GFB C16 H25 N5 O15 P2 C[C@H]1[C@....
6 5KY0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 5KY8 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 5KY9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 5KY4 - 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 : 5KY9; Ligand: GDP; Similar sites found with APoc: 105
This union binding pocket(no: 1) in the query (biounit: 5ky9.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 3LF0 ATP None
2 3IU9 T07 1.38889
3 4R84 CSF 1.40845
4 3NZ1 3NY 1.53257
5 3F3E LEU 1.69014
6 2Z3U CRR 1.88235
7 4YBN FAD 2.23214
8 4PTN PYR 2.33236
9 1OUK 084 2.53521
10 5KJW 53C 2.53521
11 4BG4 ADP 2.8169
12 4YHB FAD 2.9304
13 4TWP AXI 2.95203
14 1VJY 460 3.30033
15 5W4W 9WG 3.32326
16 4KBA 1QM 3.32326
17 4TXE 38F 3.40136
18 5UIU 8CG 3.40557
19 6CDO ALA VAL GLY ILE GLY ALA VAL PHE 3.47826
20 4JEM C5P 3.52941
21 2YN4 39J 3.81356
22 2DXU BT5 3.82979
23 3BRE C2E 3.94366
24 4K7O EKZ 4.16667
25 4CQE CQE 4.31655
26 3EM0 CHD 4.34783
27 5MW4 5JU 4.49102
28 2IHK CSF 4.50704
29 1Q11 TYE 4.78873
30 4RF7 ARG 5
31 5JFL NAD 5
32 3G5D 1N1 5
33 3ETG NDP 5
34 3ETG GLU 5
35 3CYQ AMU 5.07246
36 5F6U 5VK 5.09554
37 2JK0 ASP 5.23077
38 4AVV CD 5.39216
39 2J4D MHF 5.6338
40 6GNO XDI 5.92593
41 1V6A TRE 6.0241
42 1TE2 PGA 6.63717
43 3SAO DBH 6.875
44 4OYA 1VE 7.04225
45 3ZO7 K6H 7.44681
46 1IIM TTP 7.5
47 1QH9 LAC 7.5
48 1H5T DAU 7.5
49 4Z87 GDP 7.5
50 3A70 NPO 7.5
51 2ZWI C5P 7.5
52 6FA4 D1W 7.88732
53 4P83 U5P 8.24176
54 5ZA2 NXL 8.4507
55 2VGD XYP XYP 10
56 2WSA MYA 10
57 2WSA 646 10
58 1SDW IYT 10
59 4L8F MTX 10.2564
60 1V3S ATP 10.3448
61 1REQ DCA 11.5493
62 5KOR GDP 12.5
63 1F9V ADP 12.5
64 1H8P PC 12.5
65 1RYD GLC 12.5
66 4P5Z Q7M 12.5
67 2HIM ASP 12.5
68 2HIM ASN 12.5
69 2XVD AS6 12.5
70 5ICE SAH 12.5
71 1AOE NDP 12.5
72 1AOE GW3 12.5
73 4B2Z P5S 12.5
74 5W3Y ACO 12.5
75 5UGH 8AJ 12.5
76 1Y7P RIP 13.4529
77 2AGC DAO 15
78 5X7Q GLC GLC GLC 15
79 5LXT GTP 15
80 5X7Q GLC GLC GLC GLC 15
81 6G9I CXX 15
82 4MIB 28M 15
83 3HKW IX6 15
84 3PP0 03Q 15
85 6F5W KG1 15
86 4R8L ASP 15
87 1GPM AMP 15
88 1FFU CDP 15
89 2QHS OCA 15
90 2JFN GLU 15.0877
91 2QHV OC9 16.6667
92 4WCX MET 17.5
93 1LSH PLD 17.5
94 3VZ3 NAP 17.5
95 3VSV XYS 20
96 3CBC DBS 20
97 2J9D ADP 20
98 5KF6 NAD 22.5
99 1YFS ALA 25
100 4WOE ADP 27.5
101 5HCY 60D 27.5
102 4GDX GLU 27.5
103 1OFL NGK GCD 30
104 3SIX GDP 37.5
105 5L2R MLA 42.5
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