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Receptor
PDB id Resolution Class Description Source Keywords
5A07 1.9 Å EC: 2.-.-.- X-RAY STRUCTURE OF THE MANNOSYLTRANSFERASE KTR4P FROM S. CER IN COMPLEX WITH GDP SACCHAROMYCES CEREVISIAE TRANSFERASE GOLGI APPARATUS MANNOSYLTRANSFERASES GT-A MEPROTEINS
Ref.: STRUCTURE OF THE GLYCOSYLTRANSFERASE KTR4P FROM SACCHAROMYCES CEREVISIAE PLOS ONE V. 10 36239 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP B:500;
A:500;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MN B:501;
A:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
ACT A:1465;
B:1465;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5A07 1.9 Å EC: 2.-.-.- X-RAY STRUCTURE OF THE MANNOSYLTRANSFERASE KTR4P FROM S. CER IN COMPLEX WITH GDP SACCHAROMYCES CEREVISIAE TRANSFERASE GOLGI APPARATUS MANNOSYLTRANSFERASES GT-A MEPROTEINS
Ref.: STRUCTURE OF THE GLYCOSYLTRANSFERASE KTR4P FROM SACCHAROMYCES CEREVISIAE PLOS ONE V. 10 36239 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 5A07 - GDP C10 H15 N5 O11 P2 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 237 families.
1 5A07 - GDP C10 H15 N5 O11 P2 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 187 families.
1 5A07 - 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 : 5A07; Ligand: GDP; Similar sites found with APoc: 111
This union binding pocket(no: 1) in the query (biounit: 5a07.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2O4C NAD 1.31579
2 4L9Z COA 1.47493
3 2BO4 FLC 1.51134
4 3CKJ CIT 1.51976
5 3W54 RNB 1.51976
6 5FAG PPI 1.70732
7 4JAL SAH 1.79641
8 3AYI HCI 1.84332
9 3AYI FAD 1.84332
10 5N2D 8J8 2.08333
11 9LDB NAD 2.10843
12 5MM0 GDD 2.13904
13 5NDF LU2 2.30415
14 5NDF UDP 2.30415
15 2FFU UDP 2.30415
16 5AJP UDP 2.30415
17 3HAZ FAD 2.30415
18 5NIU 8YZ 2.34375
19 3THR C2F 2.38908
20 4MDH NAD 2.39521
21 1JGT CMA 2.53456
22 1JGT APC 2.53456
23 2YQS UD1 2.53456
24 3ZF8 GDP 2.62295
25 1RJW ETF 2.65487
26 3G6K POP 2.92208
27 3G6K FAD 2.92208
28 2P69 PLP 2.94118
29 4E5N NAD 3.0303
30 2CVQ NDP 3.0581
31 1LDN NAD 3.16456
32 2D7I UDP 3.22581
33 4NMC FAD 3.22581
34 4NMC 2OP 3.22581
35 2YN4 39J 3.38983
36 1GPM AMP 3.45622
37 1GUZ NAD 3.54839
38 5DCH 1YO 3.64583
39 3GYQ SAM 3.67647
40 3II1 BGC 3.68664
41 4YCA NDP 3.7415
42 4NAT 2W5 3.75
43 4NAT ADP 3.75
44 3A16 PXO 3.75335
45 4L2I NAD 3.75723
46 4L2I FAD 3.75723
47 1VM6 NAD 3.94737
48 5N2F 8HW 4.03226
49 1O94 AMP 4.16667
50 1O97 AMP 4.16667
51 1O97 FAD 4.16667
52 2VBQ BSJ 4.24242
53 4CNG SAH 4.31373
54 3CV3 UDP 4.4335
55 5A7Y SAH 4.48718
56 1C3V NDP 4.4898
57 3DTU DXC 4.60829
58 1NHX PEP 4.60829
59 1NHX FTB 4.60829
60 3VQ2 LP4 LP5 MYR DAO 4.60829
61 3BQD DAY 4.70588
62 1QX4 FAD 4.74453
63 3BBH SFG 4.87805
64 1JV1 UD1 5.06912
65 5FJN BE2 5.29954
66 5FJN FAD 5.29954
67 2C5S AMP 5.32688
68 1L5Y BEF 5.80645
69 4O8A FAD 5.99078
70 1TIW FAD 5.99078
71 1TIW TFB 5.99078
72 5KF6 FAD 5.99078
73 5KF6 TFB 5.99078
74 1PVN MZP 6.11702
75 6IS0 SAH 6.2212
76 1EFV AMP 6.27451
77 1EFV FAD 6.27451
78 5NUE NAD 6.3253
79 5NUF NAD 6.3253
80 5ZBC FAD 6.45161
81 3DMH GMP 6.56168
82 3DMH SAM 6.56168
83 1V2X SAM 6.70103
84 1N07 ADP 6.74847
85 5G3U FDA 6.85579
86 4RYV ZEA 7.09677
87 2BOS GLA GAL GLC NBU 7.35294
88 2BOS GLA GAL GLC 7.35294
89 4R2M ANP 7.59494
90 1XL8 OCB 8.06452
91 5TWJ SAM 8.64198
92 5O96 SAM 8.97959
93 1HYH NAD 9.70874
94 1YUC EPH 9.80392
95 2OQ2 A3P 10.3448
96 4H6Q TFB 10.5769
97 4H6Q FAD 10.5769
98 6H8S FSZ 11.6279
99 2O07 MTA 13.4868
100 2O07 SPD 13.4868
101 1C4Q GLA GAL BGC 14.4928
102 2BL9 NDP 15.126
103 2BL9 CP6 15.126
104 1QF9 ADP 16.4948
105 1QF9 ALF 16.4948
106 1QF9 C5P 16.4948
107 3NK7 SAM 16.6065
108 2Y69 CHD 18.6047
109 5ZCO CHD 18.8235
110 5W97 CHD 18.8235
111 3QF7 ANP 20
Pocket No.: 2; Query (leader) PDB : 5A07; Ligand: GDP; Similar sites found with APoc: 11
This union binding pocket(no: 2) in the query (biounit: 5a07.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 9LDT NAD 2.10843
2 1VBO MAN MAN MAN 2.68456
3 5M42 FMN 3.22581
4 3WLE NAD 3.51906
5 1MFI FHC 4.38596
6 4M1U MBG A2G 5.71429
7 1RM0 NAI 6.45161
8 1N07 FMN 6.74847
9 2G37 FAD 7.95107
10 1JNR FAD 8.29493
11 2FKA BEF 14.7287
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