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...
View in 3D viewer
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: 153
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 G 0.828947 0.986486
7 5GP 0.828947 0.986486
8 G1R 0.82716 0.986667
9 GCP 0.82716 0.973684
10 GSP 0.817073 0.948718
11 GAV 0.797619 0.961039
12 GMV 0.792683 0.973684
13 G2P 0.77381 0.961039
14 G2R 0.770115 0.961039
15 GDP MG 0.759036 0.923077
16 GP2 0.756098 0.961039
17 GDP BEF 0.75 0.9
18 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GDC 0.747253 0.961039
21 GPG 0.741573 0.961039
22 G3D 0.732558 0.986486
23 ALF 5GP 0.729412 0.888889
24 Y9Z 0.728261 0.902439
25 GTP MG 0.724138 0.923077
26 BEF GDP 0.724138 0.888889
27 G5P 0.723404 0.973684
28 GFB 0.72043 0.961039
29 GTG 0.72043 0.936709
30 GDR 0.72043 0.961039
31 G4P 0.715909 0.986486
32 GCP G 0.715909 0.935065
33 6CK 0.712766 0.936709
34 G3A 0.712766 0.973684
35 GDP ALF 0.7 0.888889
36 GDP AF3 0.7 0.888889
37 YGP 0.698925 0.901235
38 JB2 0.697917 0.961039
39 GKD 0.697917 0.961039
40 GDX 0.690722 0.973684
41 GPD 0.690722 0.925
42 GMP 0.684211 0.88
43 0O2 0.666667 0.986486
44 G G 0.659574 0.935065
45 JB3 0.656863 0.948718
46 NGD 0.650485 0.961039
47 GDP 7MG 0.636364 0.911392
48 DGI 0.636364 0.923077
49 U2G 0.634615 0.936709
50 GPX 0.634409 0.946667
51 IDP 0.632184 0.972973
52 2MD 0.632075 0.891566
53 CAG 0.62963 0.880952
54 CG2 0.622642 0.936709
55 FEG 0.619048 0.879518
56 MGD 0.614679 0.891566
57 ZGP 0.613208 0.869048
58 GH3 0.612903 0.973333
59 3GP 0.611765 0.946667
60 MD1 0.607143 0.891566
61 PGD 0.59292 0.925
62 DGT 0.591398 0.923077
63 BGO 0.588785 0.924051
64 TPG 0.582609 0.840909
65 DBG 0.582609 0.948718
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 I2C FE2 CMO CMO 0.566372 0.808989
69 G A A A 0.553571 0.923077
70 MGP 0.553191 0.961039
71 U A G G 0.548673 0.935065
72 G4M 0.548387 0.880952
73 6G0 0.547368 0.961039
74 G1R G1R 0.542373 0.924051
75 P2G 0.527473 0.883117
76 PGD O 0.525 0.850575
77 ADP 0.522222 0.92
78 GGM 0.517544 0.901235
79 DG 0.516484 0.910256
80 DGP 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G G U 0.509259 0.935065
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 G C 0.504348 0.9
86 GPC 0.491525 0.879518
87 G7M 0.483871 0.948052
88 6AD 0.479592 0.841463
89 ATP 0.473684 0.92
90 G2Q 0.471154 0.961039
91 U G A 0.469697 0.888889
92 5FA 0.46875 0.92
93 AQP 0.46875 0.92
94 GTA 0.468468 0.936709
95 7DD 0.468085 0.906667
96 G G G RPC 0.466102 0.875
97 SGP 0.463158 0.82716
98 01G 0.462963 0.902439
99 B4P 0.457447 0.894737
100 AP5 0.457447 0.894737
101 A2D 0.456522 0.894737
102 G G G C 0.455285 0.9125
103 ACQ 0.454545 0.896104
104 5GP 5GP 0.454545 0.883117
105 ANP 0.454545 0.896104
106 A G C C 0.451613 0.911392
107 APC G U 0.45082 0.886076
108 G U34 0.449153 0.888889
109 DG DG 0.448598 0.865854
110 ITT 0.447917 0.868421
111 BA3 0.446809 0.894737
112 35G 0.444444 0.933333
113 C2E 0.444444 0.921053
114 PCG 0.444444 0.933333
115 MGO 0.441176 0.864198
116 AN2 0.4375 0.907895
117 G C C C 0.4375 0.924051
118 M33 0.43299 0.883117
119 UCG 0.429688 0.911392
120 A G U 0.42963 0.888889
121 ACP 0.428571 0.896104
122 MGQ 0.424528 0.935897
123 7DT 0.424242 0.906667
124 APR 0.424242 0.894737
125 AR6 0.424242 0.894737
126 93A 0.42268 0.833333
127 A4P 0.420168 0.869048
128 SAP 0.42 0.873418
129 AD9 0.42 0.896104
130 AGS 0.42 0.873418
131 G8D 0.42 0.875
132 CA0 0.418367 0.896104
133 ATF 0.417476 0.884615
134 AGO 0.414634 0.888889
135 NIA 0.413043 0.82716
136 MGV 0.412844 0.890244
137 TAT 0.411765 0.884615
138 A1R 0.411215 0.839506
139 ADQ 0.411215 0.871795
140 RGT 0.410714 0.909091
141 CGP 0.409836 0.86747
142 AMP 0.408602 0.893333
143 A 0.408602 0.893333
144 UP5 0.40678 0.873418
145 C2R 0.406593 0.906667
146 AMZ 0.406593 0.918919
147 JBT 0.405882 0.778947
148 A22 0.40566 0.907895
149 25L 0.405405 0.907895
150 ADX 0.40404 0.809524
151 8OD 0.401961 0.946667
152 4TC 0.4 0.851852
153 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KY9; Ligand: GDP; Similar sites found: 45
This union binding pocket(no: 1) in the query (biounit: 5ky9.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3IU9 T07 0.02547 0.40696 1.38889
2 4R84 CSF 0.002592 0.42663 1.40845
3 3F3E LEU 0.009054 0.42929 1.69014
4 1OUK 084 0.02429 0.43986 2.53521
5 4LOO SB4 0.002714 0.4279 2.53521
6 5IXJ THR 0.0366 0.40001 2.53521
7 4YHB FAD 0.01829 0.40125 2.9304
8 4TWP AXI 0.02805 0.4094 2.95203
9 1VJY 460 0.009024 0.42258 3.30033
10 4KBA 1QM 0.004702 0.42616 3.32326
11 5W4W 9WG 0.008619 0.41378 3.32326
12 4TXE 38F 0.004536 0.40596 3.40136
13 5UIU 8CG 0.01636 0.40757 3.40557
14 2YN4 39J 0.008477 0.42404 3.81356
15 3BRE C2E 0.01148 0.4116 3.94366
16 4CQE CQE 0.01758 0.41398 4.31655
17 5MW4 5JU 0.02471 0.40458 4.49102
18 3JUT GTQ 0.01376 0.40162 4.61538
19 3G5D 1N1 0.02974 0.41503 5
20 5JFL NAD 0.01563 0.40853 5
21 2J4D MHF 0.01974 0.40295 5.6338
22 4OYA 1VE 0.01429 0.43696 7.04225
23 4AFK FLC 0.009702 0.41569 7.5
24 4DSU BZI 0.007311 0.42657 9.52381
25 2VGD XYP XYP 0.005005 0.44305 10
26 2WSA MYA 0.04765 0.41774 10
27 2WSA 646 0.04765 0.41774 10
28 1REQ DCA 0.03746 0.40301 11.5493
29 5KOR GDP 0.0000001947 0.62329 12.5
30 4P5Z Q7M 0.01807 0.41339 12.5
31 5UGH 8AJ 0.008054 0.40211 12.5
32 1Y7P RIP 0.001064 0.48353 13.4529
33 3HKW IX6 0.03521 0.40908 15
34 2QHS OCA 0.01289 0.40059 15
35 1GPM AMP 0.024 0.40038 15
36 2QHV OC9 0.01169 0.40689 16.6667
37 4WCX MET 0.008892 0.40703 17.5
38 3VZ3 NAP 0.02394 0.40195 17.5
39 3VSV XYS 0.006687 0.42647 20
40 2J9D ADP 0.01092 0.40569 20
41 5KF6 NAD 0.02677 0.4007 22.5
42 1YFS ALA 0.009988 0.42606 25
43 5HCY 60D 0.0131 0.42519 27.5
44 4GDX GLU 0.02049 0.40385 27.5
45 3SIX GDP 0.0000001969 0.61883 37.5
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